Macrocyclic kinase inhibitors

Compounds of Formula (I): wherein variables are defined herein, and pharmaceutically acceptable salts, synthesis, intermediates, formulations, and methods of disease treatment therewith, including cancers for which FAK inhibition is beneficial.

FIELD AND BACKGROUND

The present invention pertains in large part to cancer treatment, targeted therapies, tyrosine kinase inhibitors, certain chemical compounds, chemical syntheses, compositions, and methods of treating, e.g., tumors and other cancers with the compounds, including conditions in which FAK plays a significant role or FAK inhibition can be beneficial.

Focal adhesion kinase (FAK) is a cytoplasmic tyrosine kinase which plays a major role in the transduction of the signal transmitted by integrins, a family of heterodimeric receptors for cell adhesion. FAK and integrins are colocalized in perimembrane structures called adhesion plaques.

FAK signaling through ERK, PI3K, and p130cas is important in cancer cell proliferation, survival, and migration. pFAK and/or FAK overexpression has been reported in many cancer tumors. An increase in the proliferation of tumor cells in vivo has been observed after induction of the expression of FAK in human astrocytoma cells. Cary et al.,J. Cell Sci.,109:1787-94 (1996). FAK is overexpressed in prostate, breast, thyroid, colon, melanoma, brain and lung cancers, the level of FAK expression being directly correlated with tumors exhibiting the most aggressive phenotype. Weiner et al.,Lancet,342(8878):1024-25 (1993); Owens et al.,Cancer Res.,55:2752-55 (1995); Maung et al.,Oncogene,18:6824-28 (1999); Wang et al.,J. Cell Sci.,113:4221-30 (2000). FAK is highly active in human epithelial and mesenchymal tumors such as melanoma, lymphoma, and multiple myeloma. Increased FAK correlates with increased invasiveness and increased ability of cancer to metastasize.

Inhibition of FAK signaling in vitro induces cell growth arrest, reduces motility, and can cause cell death. KD-FAK and DN-FAK have been shown to inhibit tumor growth in vivo. FAK is also known as PTK2.

In hepatocytes, TGFβ induces a Src-dependent activation of FAK; and there is evidence that FAK signaling is required for transcriptional up-regulation of mesenchymal and invasiveness markers and for delocalization of membrane-bound E-cadherin.Exp. Cell Res.,314, 143-52 (2008).

There remains a need for new kinase inhibitors, including FAK inhibitors, having the potential to reach the clinic and regulatory approval for treating disease such as cancer, among others.

SUMMARY

In some aspects, the present invention concerns compounds of Formula I, as shown below:

X is N or CH;

when Q1and Q4are independently CH or N, an optionally substituted5-6cyclic containing one or more heteroatoms is optionally fused to Ring A2at Q1and Q4;

R1, Ra, and Rbare each independently H or an optional substituent; and

or a pharmaceutically acceptable salt thereof.

In some aspects, compounds of the invention are inhibitors of kinases, including FAK. In some aspects, compounds of the invention are selective inhibitors of FAK.

In some aspects, the invention includes methods treating proliferative disease, particularly cancers, including cancers mediated or driven at least in part by FAK, or for which FAK inhibition may be beneficially, alone or in combination regimens with other agents. In some embodiments FAK overexpression or pFAK may be implicated.

The invention includes the compounds and salts thereof, any physical forms thereof including solvates and hydrates, preparation of the compounds, intermediates, and pharmaceutical compositions and formulations thereof.

DETAILED DESCRIPTION

Compounds

In some aspects, the invention includes the compounds and salts thereof of Formula I, above, wherein (Subgenus 1):

A1is phenylene or5-6heteroaryl either of which is optionally substituted by one or more independent R5;

A3is5-6heterocyclic optionally substituted by one or more independent R6;

L3is C2-6aliphatic optionally substituted by one or more independent R9;

L4is C1-3aliphatic optionally substituted by one or more independent R8;

when Q1and Q4are independently CH or N, an optionally substituted5-6cyclic containing one or more heteroatoms is optionally fused to Ring A2at Q1and Q4;

Raand Rbare each independently selected from H, C1-6aliphatic, C3-6carbocyclic, or4-6heterocyclic, any of which can be substituted by one or more independent Raa;

each R9is independently selected from H, oxo, halogen C1-6aliphatic, C3-6cycloaliphatic,3-6-spirocyclic (optionally substituted by one or more independent R26), —OC0-6aliphatic, —NR10R11, —S(O)0-2R12, —S(O)2NR10R11, —C(O)NR10R11, —C(O)OR13, or —NR10S(O)0-2R12;R10, R11, R12, and R13are independently selected from H, C1-6aliphatic, or C3-6cycloaliphatic, wherein R10and R11attached to the same atom can be taken together with the atoms to which they are attached to form a ring containing one or more heteroatoms;

R20and R21are independently selected from H, —OR23, —S(O)0-2R28, —NO2, C1-6aliphatic, or3-10cyclic; wherein any of the foregoing is optionally substituted by one or more independent R7groups;

each R22is independently selected from H, halo, —NR24R25, C1-6aliphatic, or3-10cyclic; wherein any of the foregoing is optionally substituted by one or more independent R7groups;

each R23is independently selected from H, C1-6aliphatic, or3-10cyclic; wherein any of the foregoing is optionally substituted by one or more independent R7groups;

R26and R27are each independently selected from the group consisting of —H, C1-6aliphatic, or3-10cyclic; wherein any of the foregoing is optionally substituted by one or more independent halo, —CF3, —CN, —NO2, —OH, —O(C1-6aliphatic), —C(O)C1-6aliphatic,3-10cyclic, —SH, —S(C1-6aliphatic), —NH2, —NH(C1-6aliphatic), or —N(C1-6aliphatic)2groups;

each R28is independently selected from H, —NR24R25, —C(O)R24, —CF3, C1-6aliphatic, or3-10cyclic; wherein any of the foregoing is optionally substituted by one or more independent R7groups;

wherein one or two carbon ring atoms in each of the aforementioned cyclic groups is optionally and independently replaced with C(O) or C(S);

wherein two groups attached to the same tetravalent carbon atom in each of the aforementioned cyclic and aliphatic groups are optionally joined to form a ring system.

In some aspects, the invention includes the compounds of Formula I and salts thereof, above, wherein (Subgenus 2):

X is N or CH;

A1is phenylene or5-6heteroaryl either of which is optionally substituted by one or more independent R5;

A3is5-6heterocyclic optionally substituted by one or more independent R6;

L3is C2-6aliphatic optionally substituted by one or more independent R9;

L4is C1-3aliphatic optionally substituted by one or more independent R8;

wherein an optionally substituted5-6cyclic optionally containing one or more heteroatoms is optionally fused to Ring A2at Q1and Q4;

Raand Rbare each independently selected from H, C1-6aliphatic, including C3-6-carbocyclic, or4-6heterocyclic, any of which can be substituted by one or more independent Raa;

each R10, R11, R12, and R13is independently selected from H, C1-6aliphatic, including C3-6-carbocyclic, wherein R10and R11attached to the same atom can be taken together to form a ring containing one or more heteroatoms;

R26and R27are each independently selected from the group consisting of —H, C1-6aliphatic, or3-10cyclic; wherein any of the foregoing is optionally substituted by one or more independent halo, —CF3, —CN, —NO2, —OH, —O(C1-6aliphatic), —C(O)C1-6aliphatic,3-10cyclic, —SH, —S(C1-6aliphatic), —NH2, —NH(C1-6aliphatic), or —N(C1-6aliphatic)2groups;

wherein one or two carbon ring atoms in each of the aforementioned cyclic groups is optionally and independently replaced with C(O) or C(S);

wherein two groups attached to the same tetravalent carbon atom in each of the aforementioned cyclic and aliphatic groups are optionally joined to form a ring system.

In some aspects, the invention includes the compounds and salts thereof of Formula I, above, wherein (Subgenus 3):

X is N or CH;

A1is phenylene or5-6heteroaryl either of which is optionally substituted by one or more independent R5;

A3is5-6heterocyclic optionally substituted by one or more independent R6;

L3is C2-6aliphatic optionally substituted by one or more independent R9;

L4is C1-3aliphatic optionally substituted by one or more independent R8;

an optionally substituted5-6cyclic containing one or more heteroatoms is optionally fused to Ring A2at Q1and Q4;

Raand Rbare each independently selected from H, C1-6aliphatic, C3-6carbocyclic, or4-6heterocyclic, any of which can be substituted by one or more independent halo or C1-6aliphatic;

each R6, R10, R11, R12, R13, R20, R21, and R22is independently selected from H, C1-6aliphatic, or C3-6carbocyclic, wherein R10and R11or R20and R21attached to the same atom can be taken together to form a ring containing one or more heteroatoms;

In some aspects, the invention includes the compounds and salts thereof of Formula I or of any of Subgenera 1-3, above, wherein (Subgenus 4): X is N.

In some aspects, the invention includes the compounds and salts thereof of Formula I or of any of Subgenera 1-4, above, wherein (Subgenus 5): R1is selected from Cl, —CN, —NO2, or —CF3.

In some aspects, the invention includes the compounds and salts thereof of Formula I or of any of Subgenera 1-4, above, wherein (Subgenus 6): R1is —CF3.

In some aspects, the invention includes the compounds and salts thereof of Formula I or of any of Subgenera 1-6, above, wherein (Subgenus 7): Raand Rbare independently selected from H or C1-3aliphatic.

In some aspects, the invention includes the compounds and salts thereof of Formula I or of any of Subgenera 1-7, above, wherein (Subgenus 8): R4is selected from —OH, C1-4aliphatic, or —OC1-3aliphatic.

In some aspects, the invention includes the compounds and salts thereof of Formula I or of any of Subgenera 1-8, above, wherein (Subgenus 9): A3is a 5-membered heteroaryl ring that is optionally substituted by one or more independent halo, —CF3, —CN, —NO2, —OH, —O(C1-6aliphatic), —C(O)R26, —C(o)NR26R27, —S(O)0-2R26, —S(O)0-2NR26R27,3-10cyclic, —SH, —S(C1-6aliphatic), —NH2, —NH(C1-6aliphatic), or —N(C1-6aliphatic)2groups.

In some aspects, the invention includes the compounds and salts thereof of Formula I or of any of Subgenera 1-8, above, wherein (Subgenus 10): A3is a 5-membered heteroaryl ring that is optionally substituted by one or more C1-3aliphatic.

In some aspects, the invention includes the compounds and salts thereof of any of Subgenera 1-10, above, wherein (Subgenus 11): L3is C2-4aliphatic that is optionally interrupted by one or more heteroatoms and is optionally substituted by one or more oxo, C1-6aliphatic, C3-6-carbocyclic, —OC0-6aliphatic, —S(O)2R12, —S(O)2NR10R11, —C(O)NR10R11, —C(O)OR13; —NR10S(O)2R12, or —NR10R11.

In some aspects, the invention includes the compounds and salts thereof of any of Subgenera 1-10, above, wherein (Subgenus 12): L3is C3-4aliphatic that is optionally substituted by one or more oxo, —C1-6aliphatic, C3-6carbocyclic, —OC0-6aliphatic, —S(O)2R12, —S(O)2NR10R11, —C(O)NR10R11, —C(O)OR13; —NR10S(O)2R12, or —NR10R11.

In some aspects, the invention includes the compounds and salts thereof of Formula I or of any of Subgenera 1-12, above, wherein (Subgenus 13): L4is C1-2aliphatic.

In some aspects, the invention includes the compounds and salts thereof of Formula I or of any of Subgenera 1-13, above, wherein (Subgenus 14): A1is phenylene optionally substituted by one or more halo, C1-3aliphatic, or —OC1-3aliphatic, either of which is optionally substituted by one or more halo.

In some aspects, the invention includes the compounds and salts thereof of any of Subgenera 1-14, above, wherein (Subgenus 15): each R2is independently selected from H, halo, C1-2aliphatic or —OC1-2aliphatic.

In some aspects, the invention includes the compounds and salts thereof of any of Subgenera 1-14, above, wherein (Subgenus 16):

when R3is —C(O)NR10R11, R10may be taken with R2to form a ring containing one or more heteroatoms and fused to Ring A2.

In some aspects, the invention includes the compounds and salts thereof of any of Subgenera 1-15, above, wherein (Subgenus 17):

In some aspects, the invention includes the compounds and salts thereof of any of Subgenera 1-2, above, wherein (Subgenus 18):

A1is phenylene optionally substituted by halo, —C1-3aliphatic, or —OC1-3aliphatic, either of which is optionally substituted by one or more halo or —OCF3;

A3is a 5-membered heteroaryl ring that is optionally substituted by one or more C1-3aliphatic;

L3is C2-4aliphatic optionally substituted by one or more C1-6aliphatic or C3-6carbocyclic;

wherein R2and R3are optionally taken together to define an optionally substituted5-6cyclic fused at Q1and Q4to Ring A2and containing one or more heteroatoms;

or R10and R11attached to the same atom can be taken together with the atoms to which they are attached to form a ring containing one or more heteroatoms.

In some aspects, the invention includes the compounds and salts thereof of Subgenus 18, above, wherein (Subgenus 19):

L3is C3-4aliphatic optionally substituted by one or more of C1-2aliphatic, —OH, or —OCH3;

R10and R11are independently C0-6aliphatic, which R10and R11of a given substituent can be taken together at any of their atoms to form a ring containing one or more heteroatoms;

or alternatively R3and Q1define any optionally substituted5-6cyclic containing one or more heteroatoms.

In some aspects, the invention includes the compounds and salts thereof of Subgenera 1 or 2, above, having the Formula II, wherein (Subgenus 20):

A3is selected from one of:

wherein the upper dotted line is a bond to A2and the lower dotted line is a bond to L3, and each X3is independently selected from N, O, or S;

L3is C2-4aliphatic that is optionally substituted by one or more C1-2aliphatic;

Q1is N or CR2;

and Q1and R3optionally define a5-6cyclic fused to ring A2and optionally containing one or more heteroatoms of which each N atom is optionally substituted with an independent C1-2aliphatic;

each R7 is independently H or C1-3aliphatic;

each R10and R11is independently H, —OCH3, or C1-3aliphatic, and R10and R11can be taken together to form a ring optionally containing one or more additional heteroatoms.

In some aspects, the invention includes the compounds and salts thereof of Subgenera 1 or 2, above, having the Formula III, wherein (Subgenus 21):

Q1is N or CR2;

R5is H or —OCH3;

each R10and R11are independently H, —OCH3, or C1-3aliphatic, and R10and R11can be taken together to form a ring optionally containing one or more additional heteroatoms.

In some aspects, the invention includes the compounds and salts thereof of Subgenera 20 or 21, above, having the following formula (Subgenus 22):

In some aspects, the invention includes the compounds and salts thereof of Subgenera 20 or 21, above, wherein (Subgenus 23):

In some aspects, the invention includes the compounds and salts thereof of Subgenera 20-23, above, wherein (Subgenus 24): Q1is N.

In some aspects, the invention includes the compounds and salts thereof of any of the foregoing recitations, which exhibits inhibition of FAK in a cellular assay with an IC50of about 100 nM or less.

In some aspects, the invention includes the compounds of Formula I selected from any one of the examples herein or a pharmaceutically acceptable salt thereof.

In some aspects, the invention includes the compounds of Formula I, which is present as a material in substantially enantiomerically pure form.

In some aspects, the invention includes the compounds of Formula I, which is present as a material in substantially pure form.

Each variable definition above includes any subset thereof and the compounds of Formula I include any combination of such variables or variable subsets.

In some aspects, the invention includes any of the compound examples herein and pharmaceutically acceptable salts thereof.

In some embodiments, the compound is selected from any one of the examples herein or a pharmaceutically acceptable salt thereof.

The invention includes the compounds and salts thereof, and their physical forms, preparation of the compounds, useful intermediates, and pharmaceutical compositions and formulations thereof.

The invention includes the isomers of the compounds. Compounds may have one or more asymmetric carbon atoms can exist as two or more stereoisomers. Where a compound of the invention contains an alkenyl or alkenylene group, geometric cis/trans (or Z/E) isomers are possible. Where the compound contains, for example, a keto or oxime group or an aromatic moiety, tautomeric isomerism (‘tautomerism’) can occur. A single compound may exhibit more than one type of isomerism.

The present invention includes any stereoisomers, even if not specifically shown, individually as well as mixtures, geometric isomers, and pharmaceutically acceptable salts thereof. Where a compound or stereocenter is described or shown without definitive stereochemistry, it is to be taken to embrace all possible individual isomers, configurations, and mixtures thereof. Thus, a material sample containing a mixture of stereoisomers would be embraced by a recitation of either of the stereoisomers or a recitation without definitive stereochemistry. Also contemplated are any cis/trans isomers or tautomers of the compounds described.

Included within the scope of the invention are all stereoisomers, geometric isomers and tautomeric forms of the inventive compounds, including compounds exhibiting more than one type of isomerism, and mixtures of one or more thereof.

When a tautomer of the compound of Formula (I) exists, the compound of formula (I) of the present invention includes any possible tautomers and pharmaceutically acceptable salts thereof, and mixtures thereof, except where specifically stated otherwise.

The compounds of the invention are not limited to those containing all of their atoms in their natural isotopic abundance. The present invention includes compounds wherein one or more hydrogen, carbon or other atoms are replaced by different isotopes thereof. Such compounds can be useful as research and diagnostic tools in metabolism pharmacokinetic studies and in binding assays. A recitation of a compound or an atom within a compound includes isotopologs, i.e., species wherein an atom or compound varies only with respect to isotopic enrichment and/or in the position of isotopic enrichment. For nonlimiting example, in some cases it may be desirable to enrich one or more hydrogen atoms with deuterium (D) or to enrich carbon with13C. Other examples of isotopes suitable for inclusion in the compounds of the invention include isotopes of hydrogen, chlorine, fluorine, iodine, nitrogen, oxygen, phosphorus, and sulfur. Certain isotopically-labeled compounds of the invention may be useful in drug and/or substrate tissue distribution studies. Substitution with heavier isotopes such as deuterium may afford certain therapeutic advantages resulting from greater metabolic stability, for example, increased in vivo half-life or reduced dosage requirements, and hence may be preferred in some circumstances. Substitution with positron emitting isotopes may be useful in Positron Emission Topography (PET) studies for examining substrate receptor occupancy.

Further, the compounds may be amorphous or may exist or be prepared in various crystal forms or polymorphs, including solvates and hydrates. The invention includes any such forms provided herein, at any purity level. A recitation of a compound per se means the compound regardless of any unspecified stereochemistry, physical form and whether or not associated with solvent or water.

The compounds of the invention may exist in both unsolvated and solvated forms. The term ‘solvate’ is used herein to describe a molecular complex comprising the compound of the invention and one or more pharmaceutically acceptable solvent molecules, for example, ethanol. The term ‘hydrate’ is employed when the solvent is water. Pharmaceutically acceptable solvates in accordance with the invention include hydrates and solvates wherein the solvent of crystallization may be isotopically substituted, e.g., D2O, d6-acetone, d 6-DMSO.

Also included within the scope of the invention are complexes such as clathrates, drug-host inclusion complexes wherein, in contrast to the aforementioned solvates, the drug and host are present in stoichiometric or non-stoichiometric amounts. Also included are complexes of the drug containing two or more organic and/or inorganic components which may be in stoichiometric or non-stoichiometric amounts. The resulting complexes may be ionized, partially ionized, or non-ionized.

The invention includes prodrugs of compounds of the invention which may, when administered to a patient, be converted into the inventive compounds, for example, by hydrolytic cleavage. Prodrugs in accordance with the invention can, for example, be produced by replacing appropriate functionalities present in the inventive compounds with certain moieties known to those skilled in the art as ‘pro-moieties’ as known in the art. Particularly favored derivatives and prodrugs of the invention are those that increase the bioavailability of the compounds when such compounds are administered to a patient, enhance delivery of the parent compound to a given biological compartment, increase solubility to allow administration by injection, alter metabolism or alter rate of excretion.

A pharmaceutically acceptable salt of the inventive compounds can be readily prepared by mixing together solutions of the compound and the desired acid or base, as appropriate. The salt may precipitate from solution and be collected by filtration or may be recovered by evaporation of the solvent. The degree of ionization in the salt may vary from completely ionized to almost non-ionized.

Synthesis

The invention includes the examples, compounds, intermediates, and synthetic methods described herein. Compounds according to the invention may be prepared according to the skill in the art and known literature in connection with the teachings herein of the examples and the following general synthetic schemes. Variables herein are not necessarily defined exactly according to Formula I herein, but are applicable thereto as is apparent in context, or can be further modified or derivatized as appropriate.

Macrocycles of the invention (Formula I) can be prepared as in Scheme 1, e.g., by intramolecular cyclization from a starting material comprising an appropriate phosphinate or phosphonate and OH-substituted L3group.

A Compound 1i can be converted to Formula I by a two-step process involving dealkylation of a phosphonate or phosphinate (Reaction 1) using NaI, TMSBr, or the like, in a solvent such as pyridine, and heating if necessary. The resulting salt can be isolated and cyclized (Reaction 2) by a coupling reaction to form an ester bond using an agent such as PyBOP, DCC, or the like, and base (e.g., DIPEA or the like) in a solvent such as DCE, pyridine, DMF, or the like, and heating if necessary.

Alternatively, a Compound 1ii can be converted to Formula I by converting the terminal OH group to a leaving group such as a tosylate or mesylate (Reaction 3), and allowing the intramolecular displacement of the newly installed leaving group by a nucleophilic moiety on A3, such as a de-protonated pyrrole nitrogen, to occur (Reaction 4). These conditions will require a base such as NaH or Na2CO3, or Cs2CO3and a solvent such as DMF or DMSO. Heating may be required. Alternatively, if A3 is a suitably acidic nucleophile, cyclization to a compound of Formula I may be achieved by using the Mitsunobu reaction with triphenylphosphine and a dialkyl azodicarboxylate in a suitable solvent such as THF or DCM.

Furthermore, Compounds of Formula I can be prepared from Compounds 1iii or 1iv via the Suzuki reaction. There are numerous Pd catalyst and ligand systems, bases and solvent combinations favorable for this transformation. These conditions can provide access to compounds wherein L2is a bond.

For example, as shown below, alkyl hydrogen phosphonates and phosphonic acids may be synthesized from the corresponding diethyl phosphonates by hydrolysis with concentrated hydrochloric acid. Stopping the reaction before complete hydrolysis occurs allows the isolation of both the alkyl hydrogen phosphonate and the phosphonic acid through chromatographic techniques such as preparative HPLC. Either of the resulting products can be isolated and cyclized according to the invention.

2,4-Di-aminopyrimidines may be synthesized through various approaches to afford target molecules. Below are non-limiting examples that the skilled artisan could utilize to realize target molecules and examples.

As in Scheme 3, commercially available or customized (See, e.g., Schemes 5-7) 5-substituted-2,4-dichloropyrimidines may be reacted directly with anilines or amines in SNAr reactions to afford mixtures of mono-substitution products (Scheme 3, 3ii/3iv). Depending on the conditions used and the nature of the aniline/amine and R1group, a predominant isomer may be formed. In these situations or under conditions of minimal regioselectivity, the isomers may be separated (fully or partially) through the use of chromatography and/or crystallization. Assignment of structure to each pure isomer may be made through NMR experiments, in particular through the use of HMBC experiments which may disclose a 3 bond H—C correlation between the C4-NH and the C5-C in the case of the 4-substituted product, which is not evident in the C2-NH isomer. Assignment of structure may be made by comparison of spectral data to those isomers made by the previous method described above or directly through NMR experimentation.

In addition to the SNAr displacements of the 2- and 4-chloro groups as indicated above, those skilled in the art will recognize that other groups may also serve as good leaving groups that may be displaced by amines and anilines under the appropriate conditions. Examples of displaceable groups include, but are not limited to alkylthio, alkylsulfonyl, bromo, trichloromethyl, fluoro, sulfonyloxy and N-benzotriazolyloxy, and in each case the 2- and 4-leaving groups may the same or different. Indeed in certain circumstances it may be preferred that the 2- and 4-displaceable groups are different as this offers the opportunity to take advantage of different leaving group potentials and so control the regiochemistry of the SNAr reaction.

Another approach to access 2-anilino, 4-anilino or 2,4-dianilino-pyrimidines involves transition metal catalyzed arylation of an aminopyrimidine, as in Scheme 4. In a typical procedure, the 2- or 4-aminopyrimidine is heated with an aryl or heteroaryl bromide or iodide in the presence of copper (I) iodide, ethylenediamine ligand and potassium carbonate base in dioxane. Other commonly used reagents are Ph2-pentadienone-Pd, NaOPh and XantPhos. Depending on the nature of the R1group at the 5-position, such reactions may be conducted on 2,4-diaminopyrimidines and some preference for one or other amino group observed. Further modification of R1may also be carried out.

In addition to refunctionalizing an activated pyrimidine system, one may also access desired derivatives through construction of the pyrimidine ring itself, as in the following:

Reaction of an appropriately substituted guanidine with an appropriately substituted β-formyl ester, β-(dimethylamino)propenoate or β-(alkoxy)propenoate yields a hydroxy pyrimidine as indicated in the above scheme. Such hydroxypyrimidines may be chlorinated using reagents such as POCl3to form intermediates analogous to those described in Scheme 3. The R1substitution in the reactants could be the same as the final R1group, or different as necessary to allow for the cyclization and/or halogenation chemistry to be successful. Where R1is different from the final R1, the interconversion to R1may be undertaken by the multiple methods known to the skilled artisan, a non-limiting list of which are described herein.

Other methods of accessing suitably functionalized pyrimidine derivatives include modification of commercially available uracil or thiouracil. For example, S-methylation of thiouracil using iodomethane and base affords an intermediate that may be functionalized at the C5 position to introduce R1, or the precursor to R1, such as Br or I. An example of such C5-functionalization is halogenation using bromine in acetic acid, N-iodosuccinimide in DMF or N-chlorosuccinimide in acetic acid, which introduces a C5 bromo-, iodo or chloro group, respectively. Groups such as CF3may be introduced through reaction with CF3I in the presence of FeSO4, H2O2and DMSO.

Also in the case of pyridines, as in Scheme 6b, modification of intermediates from this invention can provide access to a range of R1groups.

For example, the commercially available pyridine 6v can be subjected to a Buchwald Hartwig coupling with aniline 6vi to provide the intermediate 6vii. R1groups such as alkyl and cycloalkyl can be introduced by Suzuki or Negishi coupling to afford compounds of Formula 6viii. The aniline 6ix can then be installed via a second Buchwald-Hartwig reaction to afford a compound 6xi.

It may be preferable to install 6ix before introducing a new R1group as the chloro functionality of 6vii may be sensitive to those potential reaction conditions. Heating 6ix and 6vii in a polar, protic solvent with acid will give a compound 6x which can be converted to 6xi. For example, a methyl sulfone may be introduced through the L-proline-promoted CuI-catalyzed coupling of a methyl sulfinic acid salt.

C5 chemistries may also be used on uracil itself and the derivatives converted to the 4-chloro (for the thiouracil derivative) or 2,4-dichloropyrimidine derivatives through reaction with reagents such as POCl3.

Dialkylphosphonates may be prepared according to the method of Michaelis-Arbuzov as shown whereby alkyl halides or sulfonates (e.g., Hal=Br, I, Cl, OMs) are heated with trialkylphosphites. Additionally, phosphonates 8iii can be trans-esterified by first transforming them into the corresponding phosphonochloridates 8iiia by heating 8iii in SOCl2and catalytic DMF. Stirring 8iiia with a base such as DIPEA or TEA, an alcohol such as butanol or isopropanol in a solvent such as THF or DCM affords transesterified phosphonate 8iiib.

Phosphonates bearing a P-hydrogen may be reacted with alkyl halides or sulfonates (e.g., Hal=Cl, Br, I, OMs) in the presence of bases, including but not limited to Na2CO3, K2CO3, NaOH, CS2CO3, Et3N, DIPEA and DBU, and in suitable solvents, e.g., acetonitrile, DMF, dioxane, DMA to afford P-substituted products via SN2-type chemistries.

Preparation of dialkylphosphonates may be achieved via multiple approaches. For example, one dialkyl phosphonate may be converted into another, different dialkyl phosphonate. Hydrolysis of a dialkylphosphonate under acidic conditions such as concentrated hydrochloric acid affords the corresponding phosphonic acid. Other acid reagents may be used to effect this transformation including, but not limited to, HBr and HBr/HOAc. The transformation may also be achieved using basic conditions, e.g., by treatment with NaOH/MeOH or through the use of reagents such as, but not limited to, TMSI, TMSBr, TMSCl/NaI and NaI in solvents such as acetone, acetonitrile, DCM, chloroform and dioxane.

Phosphonates may be alkylated on an alpha carbon by deprotonation with strong base of which tBuOK, nBuLi, NaH and LDA are non-limiting examples, then treatment with carbon electrophiles, e.g., MeI, DMF and chloroformates (Scheme 8d) (R8and/or the other R8may be methyl). Control of the stoichiometry of the reaction components may afford mono- or dialkylated products. Additionally, sequential use of base, electrophile #1, base and electrophile #2 is another means to effectively control dialkylation.

For example, as shown below, dialkyl benzylphosphonates such as diethyl (4-nitrobenzyl)phosphonate I, may be monoalkylated at the benzylic carbon by reaction with strong base, of which LDA is a non-limiting example, followed by introduction of a suitable alkyl halide such as iodomethane. The monoalkylated product thus formed may be alkylated a second time at the benzylic carbon through deprotonation with sodium hydride and reaction with an alkyl halide such as iodomethane to yield the dialkylated material. In the instance shown below, the nitro-derived products may be reduced to the corresponding anilines via methods such as catalytic hydrogenation.

Phosphinates 8xviv can be obtained using the procedure shown in Scheme 8e. A protected phosphonite 8xiv, made from commercially available ammonium phosphinate and hexamethyldisilazide, can be alkylated with an alkyl halide to provide, in situ, the phosphinic acid 8xv. Alkyl bromide or iodides can be obtained commercially or prepared using techniques known to one skilled in the art. Compound 8xv can be alkylated with 8xvi, itself either obtained commercially or prepared using established methods, to form 8xvii. A third alkylation or coupling reaction is performed on 8xvii to form the phosphinate ester. A standard catalytic hydrogenation gives the aniline 8xviv which can be used in the chemistry, e.g., as described in Schemes 3 and 4.

Should 8xviii bear a functionality adversely affected by catalytic hydrogenation (such as chloro or bromo), alternative reduction conditions should be used. Non-limiting examples of these conditions are Fe/HCl, Fe/HOAc and SnCl2/EtOH.

Solvents appropriate for the final alkylation include polar, aprotic solvents such as DMF or NMP. Suitable bases include Na2CO3, K2CO3, or the like; coupling conditions include EDC or PYBOP, in the former case it may be advantageous to use an accelerant such as DMAP. If coupling conditions are employed the same solvents may be used or it may be preferable to use an inert solvent such as DCM or THF.

Similarly, the reaction of phosphinates bearing a P-hydrogen with alkyl halides or sulfonates (e.g., Hal=Cl, Br, I, OTf) in the presence of base also proceeds via SN2 chemistry as with phosphonates. Additionally, phosphinates 8xix can be prepared by treating the alkyl halide or sulfonate 8xviii with an alkyl phosphonite such as 8xviia, itself prepared by treating triethyl phosphite with a Grignard reagent according to the procedure of Petnehazy, et al in Synthetic Communications, 2003, 33, 1665-1674.

There may also be a desire to prepare phosphine oxides, such as via a number of methods including through the reaction of dialkyl phosphonates with carbon nucleophiles including, but not limited to, Grignard reagents.

As in the case of phosphonates and phosphinates, dialkyl phosphine oxides bearing a P-hydrogen may be reacted with alkyl halides or sulfonates (e.g., Hal=Br, I, Cl, OMs) under basic conditions or aryl halides (e.g., Hal=Br, I, Cl, OTf) under transition metal catalysis to form the P-substituted derivatives.

Other methods to access phosphine oxides include the oxidation of phosphines with oxidants such as, but not limited to, hydrogen peroxide.

Scheme 9: Functional Group Interconversion

Of general applicability, the various functionalities appearing in target molecules and examples (e.g., X at the 5-position of the pyrimidine system, or on the pendant N-aryl or N-benzyl groups), may be introduced through appropriate choice of starting materials, or where the final functionality is not available directly through this process, or where such functionality may be compromised during the subsequent chemistry to build the final molecule, alternative functionalities may be used and subsequently transformed into the final desired functionality by methods, and at points in the sequence, readily determined by one skilled in the art.

As shown in Scheme 9, nitro- or azidobenzenes may be reduced to the desired aniline compound under a range of conditions. Typically hydrogenation in the presence of a Pd/C catalyst in solvents such as methanol, ethanol, ethyl acetate will yield the desired product. In the case of the azide reduction, Staudinger conditions with Ph3P may be effectively used. Many aniline precursors are commercially available for conversion to the aniline itself. N-acyl derivatives such as amides may be hydrolyzed under acidic or basic conditions to provide the aniline. In the case of carbamates, e.g., tert-butoxycarbonyl (BOC) protected anilines, the acyl group may be removed with HCl in solvents such as dioxane or through use of TFA in DCM. FMOC protected anilines require basic conditions, typically piperidine in DMF to remove the acyl moiety.

When R is an electron withdrawing group and/or when the aromatic system is a π-deficient heterocycle, a fluoro (or other halogen or triflate), ideally conjugated to said fluoro, may be displaced under SNAr conditions with ammonia itself or an ammonia equivalent or precursor.

Aryl or heteroaryl halides and triflates may also be reacted under transition metal catalysis with ammonia equivalents or precursors to allow the introduction of nitrogen functionality. One skilled in the art will appreciate the large number of catalysts, ligands, bases and solvents cited in the extensive literature and which are commercially available for this conversion.

Intermediates of Formula 10iii can be prepared using a Suzuki coupling between an aryl or heteroaryl boronic acid of either formula 10i or 10iv and a corresponding aryl or heteroaryl halide of either formula 10ii or 10v.

Compounds of formula 10vii can be prepared from compounds of formula 10vi by Pd catalyzed installation of the boronic ester, involving the use an aryl halide, a Pd catalyst, KOAc, bis-pinacolatodiboron and an inert solvent such as dioxane or THF, typically heated.

Intermediates of Formula 10ix are non-limiting examples of compounds of Formula 10viii.

10viii (10ix) can be prepared starting with a commercially available intermediate of Formula 10x and by forming a benzoxazine-dione of Formula 10xi, performing a bromination with an agent such as NBS to give a compound of Formula 10xii. This can be transformed to the amide 10xiii by a reaction with the amine HNR20R21.

Alternatively, 10x can be esterified to form a compound of Formula 10xiv and brominated to form a compound of Formula 10xv. The amide 10xiii can be formed from 10xv by heating it, under pressure, with the amine HNR20R21in a solvent mixture such as water/methanol.

Amines of Formula 10xvi are generally commercially available or readily prepared using techniques known in the art.

Intermediates of Formula 10ii and 10iv (Scheme 10A) can be prepared from compounds of Formula 10xvii or 10xviii which are either commercially available or readily prepared by one skilled in the art, as shown in the first step of Scheme 10d, above.

The P.G. in Formula 10xviii refers to a protecting group, either a benzyl or THP in most cases, similarly, the LG in Formula 10xviii refers to either a user installed leaving group such as mesylate or tosylate, or other leaving group, e.g., bromine or iodine from a commercial material. The LG can be displaced by a nucleophilic moiety on the heterocycle A3in the presence of a base and in an appropriate solvent to form compounds of the Formula 10xx. Bases can be K2CO3 or CS2CO3, examples of an appropriate solvent is DMF or NMP. Heat may be required.

In cases where A3is not commercially available as its boronic ester, one can use a commercially available A3that has a halogen substituted on the appropriate position to prepare compounds of Formula 10xxii. Compounds 10xxii can be converted to compounds of Formula 10xx by a metal halogen exchange using a Grignard reagent (as shown) or other organometallic base such as a butyllithium species and quenching the resulting anion with a an appropriately substituted borate species.

Standard catalytic hydrogenation or an acid such as bit not limited to TsOH will remove the respective benzyl or THP protecting groups to provide 10xxi.

PREPARATIONS AND EXAMPLES

Unless otherwise noted, all materials/reagents were obtained from commercial suppliers and used without further purification.1H NMR (400 MHz or 300 MHz) and13C NMR (100.6 MHz) spectra were recorded on Bruker or Varian instruments at ambient temperature with TMS or the residual solvent peak as the internal standard. The line positions or multiples are given in ppm (δ) and the coupling constants (J) are given as absolute values in Hertz (Hz). The multiplicities in1H NMR spectra are abbreviated as follows: s (singlet), d (doublet), t (triplet), q (quartet), quint (quintet), m (multiplet), mc(centered multiplet), br or broad (broadened), AA′BB′. The signal multiplicities in13C NMR spectra were determined using the DEPT135 pulse sequence and are abbreviated as follows: +(CH or CH3), —(CH2), Cquart(C). Reactions were monitored by thin layer chromatography (TLC) on silica gel 60 F254(0.2 mm) precoated aluminum foil and visualized using UV light. Flash chromatography was performed with silica gel (400-230 mesh). Preparatory TLC was performed on Whatman LK6F Silica Gel 60 Å size 20×20 cm plates with a thickness of 1000 μm. Hydromatrix (=diatomaceous earth) was purchased from Varian.

Preparative HPLC purifications was performed on a Waters® Mass—Directed Purification System equipped with 2525 Binary Gradient Module, 2767 Sample Manager, a Column Fluidics Organizer (CFO), 2996 Photodiode Array Detector, a 515 pump for column regeneration, a reagent manager for the makeup flow, a 515 pump for at-column-dilution, ZQ™ single-quadrupole Mass Detector equipped with a Z-spray electrospray interface, controlled by MassLynx™ Version 4.1 with FractionLynx™ software. All purification work was completed using a parallel dual-column Luna C18(2) 21×150 mm, 5 μm LC/MS system and ARW (accelerated retention window). The mobile phases were water (0.1% TFA) and acetonitrile (0.1% TFA); all reagents used were of HPLC grade. The flow rate was 30 mL/min. After the columns, a 1:1000 LC packings flow splitter allowed transfer of a small portion of the eluent into the UV detector and, subsequently, a 10% portion into the ZQ MS. The electrospray source was set at 3.0 kV capillary voltage, 30 V cone voltage, 110° C. source temperature, 350° C. desolvation temperature, 600 L/h desolvation gas flow, and 60 L/h cone gas flow. For the analyzer, the multiplier was set at 550 for preparative tune method.

A solution of diethyl (3-methoxy-4-nitrobenzyl)phosphonate (Compound 1G, 1.07 g, 3.54 mmol) in ethanol (10.0 mL) was charged with palladium 10% wt on activated carbon (0.38 g). The reaction mixture was evacuated and purged with hydrogen gas (3×) and allowed to stir under hydrogen for 16 h. The reaction mixture was filtered through a pad of celite. The filtrate was concentrated under reduced pressure to afford the title compound as 0.78 g of an orange oil (80%). This material was used in successive reactions without further purification. MS (ESI): m/z 274.01 [M+H]+.

A mixture of 4-(chloromethyl)-2-methoxy-1-nitrobenzene (Compound 1H, 1.1 g, 5.46 mmol) and triethyl phosphite (1.09 g, 6.55 mmol) were heated at 100° C. for 16 h in a sealed tube. The reaction mixture was concentrated under reduced pressure to yield a black oil. The crude material was purified by silica gel chromatography on a Teledyne ISCO CombiFlash® Rf system using DCM/MeOH (100:0→95:5) as eluent to afford the title compound as 1.08 g of an orange oil (65%). MS (ESI): m/z 304.0902 [M+H]+.

An 8M solution of methylamine in ethanol (10 mL, 80 mmol) was added to a solution of methyl 3-Bromo-2-(bromomethyl)benzoate in THF (30 mL) and allowed to stir for 2 h. The reaction mixture was concentrated to dryness and the residue was triturated with water. The solids produced were collected by filtration and dried to afford 4-bromo-2-methyl-2,3-dihydroisoindol-1-one which used immediately in the next step. To a cold suspension of 4-bromo-2-methyl-2,3-dihydroisoindol-1-one (60 g, 265 mmol) in concentrated sulfuric acid (60 mL) was added pre-cooled mixture of conc. nitric acid (12.5 mL, 265 mmol) and conc. sulfuric acid (60 mL) over 20 min. The reaction mixture was stirred for 30 min at 0° C. and 2 h at room temperature. The reaction mixture was poured into an ice-water mixture (300 mL) and the precipitate that formed was collected by filtration and washed with water (3×100 mL). The solids were suspended in isopropanol (200 mL) and heated on a steam bath for 10 minutes. The mixture was cooled and the solid was collected by filtration and air dried to afford 53 g of the title compound (74%).1H NMR (CDCl3, 300 MHz) δ 3.22 (s, 3H), 4.36 (s, 2H), 7.67 (d, J=8.4 Hz, 1H), 7.78 (d, J=8.4 Hz, 1H).

To a solution of 5-bromoisatoic anhydride (4.84 g, 20.0 mmol) in THF (20 mL) was added 2M MeNH2/THF (15 mL, 30 mmol). The resulting mixture was stirred at rt overnight. The solvent was evaporated under reduced pressure and the crude material was used in next step without further purification. MS (ESI): m/z=229.03/231.06 [M+H]+. HPLC: tR=3.14 min (ZQ3: polar—5 min).

A 10M solution of Methylamine in H2O (30.0 mL, 386 mmol) was added to a stainless steel reactor containing 3-amino-6-bromopyridine-2-carboxylic acid ethyl ester (Compound 6E, 7.614 g, 31.07 mmol) in MeOH (20.0 mL). The reactor was sealed and heated to 100° C. for 16 hours. The cooled reaction mixture was transferred to a round bottom flask and concentrated in vacuo forming a yellow precipitate which was collected by filtration. Further precipitate formed in the filtrate which was also collected. The combined precipitates were dried in vacuo to afford the title compound as 6.18 g of a yellow solid.1H NMR (400 MHz, CDCl3) δ 7.80 (br. s., 1H), 7.27 (d, J=8.6 Hz, 1H), 6.91 (d, J=8.6 Hz, 1H), 6.02 (br. s., 2H), 2.97 (d, J=5.1 Hz, 3H).

A suspension of ethyl 3-aminopicolinate (Compound 6F, 4.15 g, 25.0 mmol) in H2O (30.0 mL) was treated with enough sulfuric acid to enable dissolution (˜1 mL). 2 mL of the total 10.7 mL of acetic acid to be used in this reaction was added in order to make the reaction mixture mostly homogeneous. A solution of bromine (1.29 mL, 25.0 mmol) in the remaining AcOH (8.7 mL) was added drop-wise to the vigorously stirring reaction mixture forming an orange precipitate. The mixture was allowed to stir for 15 min. The resulting thick yellow-orange suspension was filtered to collect a yellow precipitate. The filtrate was neutralized with saturated aqueous K2CO3and the additional precipitate that formed was collected by filtration and combined with the previously collected precipitate. The combined precipitates were dried and re-crystallized in EtOH (overnight in the dark) to isolate 4.24 g of pale orange crystals. The mother liquor was purified on an ISCO Combiflash system eluting with 0-5% MeOH/DCM. To isolate a further 0.58 g of the desired product for a total of 4.82 g (79%).1H NMR (400 MHz, DMSO-d6) δ 1.30 (t, J=7.1 Hz, 3H), 4.29 (q, J=7.1 Hz, 2H), 6.90 (br. s., 2H), 7.21 (d, J=8.6 Hz, 1H), 7.44 (d, J=8.8 Hz, 1H). MS (ESI): m/z 244.94 (100), 246.92 (100) [M+H]+. HPLC: tR=3.45 min (ZQ3: polar—5 min).

2-Amino-5-bromobenzoic acid (80 g, 0.37 mol) was dissolved in MeOH (600 mL) and conc. H2SO4(50 mL) was slowly added. The reaction mixture was refluxed for 72 h, then concentrated. NaOH solution was added to adjust the pH to 10-11. The mixture was extracted with EtOAc (3×500 mL). The combined organic layer was dried over MgSO4, concentrated to afford the desired compound (65 g, yield: 76%) as a colorless oil, which is used directly in the next step without purification. A mixture of methyl 2-amino-5-bromobenzoate and CH3NH2.H2O (1000 mL) was stirred at 80° C. overnight in a pressure tube. The mixture was diluted with H2O (1000 mL) and extracted with EtOAc (3×500 mL). The combined organic layers were dried over MgSO4, concentrated to afford the title compound (55 g, yield: 87%) as a gray solid.1H NMR (CDCl3, 400 MHz): δ 2.93 (d, J=5.2 Hz, 3H), 5.48 (s, br, 2H), 6.04 (s, br, 1H), 6.54 (d, J=8.4 Hz, 1H), 7.24 (dd, J=2.0, 8.4 Hz, 1H), 7.38 (d, J=2.0 Hz, 1H).

NBS (2.3 g, 12.96) was added to a cold (−8° C. to −10° C.) solution of 7-amino-2-methyl-2,3-dihydro-1H-isoindol-1-one (Compound 17E, 2 g, 12.4 mmol) in DCM (40 mL) and the mixture stirred at −8° C. to −10° C. for 1 h. A solution of 10% aq. sodium thiosulfate (30 mL) was then added to the reaction mixture and stirring was continued for another 20 minutes. The layers were separated and the aqueous layer was extracted with DCM (2×20 mL). The combined organic extracts were washed with water (3×40 mL) and brine (30 mL), and the organic layer was dried (Na2SO4) and concentrated in vacuo to yield 3.2 g of crude product. This material was triturated with ethyl acetate (10 mL) to give 2.2 g of pure 7-amino-4-bromo-2-methyl-2,3-dihydro-1H-isoindol-1-one (yield: 74%).1H NMR (CDCl3400 MHz): δ 3.14 (s, 3H), 4.20 (s, 2H), 5.20 (bs, 2H), 5.49 (d, 1H, J=8.4 Hz), 5.79 (d, 1H, J=8.4 Hz).

A solution of methylamine in ethanol (10 mL, 80 mmol, 8M solution in ethanol) was added to a solution of methyl 2-(bromomethyl)-6-nitrobenzoate (Compound 17G, 8.1 g, 29.6 mmol) in THF (30 mL). After stirring for 2 h the reaction mixture was concentrated to dryness and water (30 mL) was added with rapid stirring. The solids produced were isolated by filtration and dried to give 4.35 g of 2-methyl-7-nitro-2,3-dihydro-1H-isoindol-1-one (yield: 78%).1H NMR (CDCl3, 400 MHz): δ 3.21 (s, 3H), 4.44 (s, 2H), 7.64 (m, 2H), 7.73-7.74 (m, 1H).

Example 18 and Example 19*

Example 20 and Example 21

A solution of 2,6-Dichloro-5-trifluoromethylpyrimidine (4.76 gm, 22 mmol) in 20 mL of dichloroethane and t-butanol (1:1) was treated with a 1M solution of zinc chloride in ether (22 mL, 22 mmol) and allowed to stir at RT for 30 minutes. The mixture was subsequently cooled to 0° C. and treated with a solution of (4-amino-3-fluorobenzyl)phosphonic acid diethyl ester (Compound 22D, 3.3 g, 7.94 mmol) in dichloroethane and t-butanol (10 mL, 1:1) over 10 min through an addition funnel. After 1 hr, diisopropylethylamine (2.2 mL, 12.6 mmol) was added and the mixture was allowed to stir for 24 hours at RT. The solvents were evaporated and the residue was purified using flash column chromatography (9:1 DCM:EtOAc) to afford 3.9 g of the title compound (71%).1H NMR (600 MHz, CDCl3): δ=1.23-1.28 (m, 6H), 3.1 (d, J=22 Hz, 2H), 4.02-4.09 (m, 4H), 7.09-7.25 (m, 2H), 7.63 (s, 1H), 8.24-8.27 (m, 1H), 8.58 (s, 1H).

A solution of 4-(bromomethyl)-2-chloro-1-nitrobenzene (Compound 24F, 2.9 g, 12 mmol) in triethyl phosphite (2.6 mL, 15 mmol) was stirred at 120° C. for 16 h under nitrogen. The reaction mixture was concentrated in vacuo and the residue was purified on an Isco Combiflash eluting with 50 to 90% EtOAc in heptane to afford the title compound. MS (ES+): m/z: 308.04 [MH+]. UPLC: tR=1.33 min (UPLC-TOF: polar—3 min).

A solution of 3-chloro-4-nitrotoluene (2.0 g, 12 mmol), NBS (2.62 g, 14.6 mmol) and 2,2′-azo-bis-isobutyronitrile (0.195 g, 1.16 mmol) in α,α,α-trifluorotoluene (200 mL) was heated at 80° C. under an atmosphere of nitrogen for 3 h. Solvent was removed in vacuo and the residue was partitioned between EtOAc and water and separated. The aqueous layer was extracted with EtOAc (3×) and the combined organic fractions were washed with brine, dried over sodium sulfate, filtered, and concentrated. The crude product was taken to the next step without purification.

NBS (9.42 g, 52.9 mmol) was added to a cold (0° C.) solution of 5-fluoro-1H-benzo[d][1,3]oxazine-2,4-dione (Compound 27E, 9.2 g, 50.8 mmol) in DCM and DMF (120 mL+60 mL) over the course of 40 min. The reaction mixture was stirred at 0° C. for 2 h then allowed to warm to RT. After 30 min, the DCM was removed in vacuo. The remaining reaction mixture was cooled −10° C., treated with a solution of 2M methyl amine in THF (50.8 mL, 101.6 mmol) and allowed to stir for overnight at room temperature. The reaction mixture was poured to water (240 mL) and the resulting suspension was extracted with ethyl acetate (3×100 mL). The combined ethyl acetate layer was washed with water (3×100 mL), dried (Na2SO4) and concentrated to give crude residue which was purified by column chromatography (20% ethyl acetate/hexanes) to afford 4 g of the title compound (32% over two steps).1H NMR (CDCl3, 500 MHz) δ=2.98 (d, J=4.5 Hz, 3H), 5.90 (brs, 2H), 6.38 (d, J=9.0 Hz, 1H), 6.55 (brs, 1H), 7.24-7.27 (m, 1H).

A suspension of 4-bromo-5-fluoro-2-methyl-7-nitro-2,3-dihydro-1H-isoindol-1-one (Compound 31E, 490 mg, 1.70 mmol) in EtOH (10.0 mL) was charged with iron powder (473 mg, 8.48 mmol) and then heated to reflux. After 10 min of reflux, the reaction mixture was charged with 1 M of HCl in H2O (2.03 mL, 2.03 mmol) and stirred at reflux for 10 min. The reaction mixture was filtered through a pad of celite. The filtrate was concentrated under reduced pressure. The residue was quenched with NaHCO3(10 mL) and extracted with DCM (15 mL). The organic layer was washed with brine, dried over Na2SO4, filtered and concentrated under reduced pressure to an orange solid. The crude material was purified using a Teledyne ISCO Combiflash® Rf system using DCM/MeOH (100:0→95:5) as eluent. The fractions containing product were combined and then concentrated under reduced pressure to yield a bright yellow solid (218 mg, 50%).1H NMR (CDCl3, 400 MHz): δ 6.38 (d, J=10.9 Hz, 1H) 5.29 (br. s., 2H) 4.22 (s, 2H) 3.14 (s, 3H). MS (ESI): m/z=260.99 [M+H]+. UPLC: tR=1.26 min (UPLC-TOF: polar—3 min).

A solution of 4-bromo-5-fluoro-2-methyl-2,3-dihydro-1H-isoindol-1-one (Compound 31F, 1.5 g, 6.1 mmol) in sulfuric acid (3.0 mL, 56 mmol) was cooled in an ice bath to 0° C. and then charged with nitric acid (2.0 mL, 43 mmol). The reaction mixture was allowed to stir overnight while gradually warming to rt. The reaction mixture was quenched by adding the mixture dropwise into a separatory funnel containing ice and then extracted with DCM (15 mL). The organic layer was washed with brine (15 mL), dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure to a yellow solid. The crude material was purified using a Teledyne ISCO Combiflash® Rf system using DCM/EtOAc (100:0→90:10) as eluent to afford the product compound as a yellow solid (493 mg, 28%).1H NMR (CDCl3, 400 MHz): δ 7.60 (d, J=7.6 Hz, 1H) 4.39 (s, 2H) 3.23 (s, 3H). MS (ESI): m/z=290.96 [M+H]+. UPLC: tR=1.23 min (UPLC-TOF: polar—3 min).

The regio-isomeric mixture of Compound 31G and Compound 31H (2.02 g, 8.18 mmol) was taken up in carbon tetrachloride (40 mL) and treated with NBS (2.91 g, 16.4 mmol) and 2,2′-azo-bis-isobutyronitrile (3.12 mg, 0.019 mmol) and allowed to stir at 80° C. overnight. The reaction mixture was quenched with water (10 mL) and extracted with DCM (2×20 mL). The organic layer was washed with water (10 mL), brine (10 mL), and then dried over anhydrous sodium sulfate. The solvents were evaporated under reduced pressure to give a light-yellow oil. The product mixture was taken up in THF (15 mL) and then treated with a solution of 2.0 M of methylamine in THF (8.18 mL, 16.4 mmol) and DIPEA (2.85 mL). After stirring overnight at rt, the reaction mixture was evaporated under reduced pressure to afford a crude solid which was purified using a Teledyne ISCO Combiflash® Rf system [gradient eluent EtOAc/Heptane=50-100%) to give the desired product as 1.40 g of a white solid.1H NMR (CDCl3, 400 MHz): δ 7.77 (dd, J=8.3, 4.5 Hz, 1H), 7.24 (app t, J=8.6 Hz, 1H), 4.33 (s, 2H), 3.22 (s, 3H). MS (ESI): m/z=244.05/246.03 [M+H]+. UPLC: tR=3.33 min (ZQ3: polar—5 min).

Compound 31G and Compound 31H: Methyl 3-bromo-4-fluoro-2-methylbenzoate and Methyl 3-bromo-4-fluoro-5-methylbenzoate

n-BuLi (66.0 mmol, 41 mL of 1.6 M solution in hexanes) was added to a solution of 2,2,6,6-tetramethyl-piperidine (9.32 g, 66.0 mmol) in THF (80 mL) at −20° C. under an atmosphere of argon. The resulting mixture was stirred at this temperature for 30 min, cooled to −50° C. and then treated, drop-wise, with a solution of 3-bromo-4-fluorobenzoic acid (6.57 g, 30.0 mmol) in THF (20 mL). After 1 hour of stirring, a solution of methyl iodide (7.47 mL, 120 mmol) in THF (10 mL) was added. The mixture was slowly warmed to rt and then allowed to stir at rt overnight. The reaction was quenched with aq. NH4Cl (20 mL) and then diluted with EtOAc (100 mL). The organic layer was washed with brine (30 mL) and then dried over anhydrous sodium sulfate. The solvents were evaporated under reduced pressure to give a mixture of 1- and 5-methyl-substituted benzoic acid. This mixture was taken up in DMF (30 mL) and then treated with potassium carbonate (8.29 g, 60.0 mmol) and methyl iodide (3.74 mL, 60.0 mmol). The resulting mixture was stirred at rt overnight. The mixture was diluted with EtOAc (100 mL), washed with water (3×30 mL), brine (30 mL), and then dried over anhydrous sodium sulfate. The residue was purified using a Teledyne ISCO Combiflash® Rf system [gradient eluent EtOAc/Heptane=0-20%) to afford a mixture of the desired compounds as 2.5 g of a light-yellow oil (ratio of Compound 31G to Compound 31H is 3:1). Compound 31G:1H NMR (CDCl3, 400 MHz) δ 7.82 (dd, J=8.6, 5.6 Hz, 1H), 7.02 (app t, J=8.1 Hz, 1H), 3.91 (s, 3H), 2.71 (s, 3H).

A solution of 3-bromo-4-aminotoluene (4.0 g, 21 mmol) in THF (50 mL) was charged with di-tert-butyldicarbonate (4.7 g, 21 mmol) and stirred at reflux for 24 h. The reaction mixture was partitioned between EtOAc and water and separated. The aqueous layer was extracted with EtOAc (3×) and the combined organic fractions were washed with brine, dried over sodium sulfate, filtered, and concentrated. The compound was purified in two batches on an Isco Combiflash eluting with 0 to 10% EtOAc in heptane to afford the title compound.1H NMR (400 MHz, chloroform-d) δ 7.40-7.44 (m, 1H), 7.08-7.10 (m, 2H), 2.35 (s, 3H), 1.41 (s, 18H).

A 1M solution of zinc chloride in ether (12.8 mL, 12.8 mmol) was added to a solution of 2,6-dichloro-5-trifluoromethylpyrimidine (2.76 gm, 12.8 mmol) in 20 mL of dichloroethane and t-butanol (1:1) under an atmosphere of nitrogen. The reaction mixture was stirred at rt for 30 min, cooled to 0° C. and then treated with a solution of (4-amino-3-methyl benzyl)phosphonic acid diethyl ester (Compound 33D, 2.2 gm, 8.5 mmol) in dichloroethane and t-butanol (10 mL, 1:1) slowly over 10 min through an addition funnel. After 1 hour, diisopropylethylamine (2.2 mL, 12.6 mmol) was added and then reaction gradually warmed up to rt over 4 hrs. The reaction mixture was refrigerated overnight causing the desired product to precipitate out of solution. This was collected by filtration to afford 2.7 g of the title compound (73%).1H NMR (300 MHz, CDCl3): δ 1.21-1.26 (m, 6H), 2.3 (s, 3H), 3.15 (d, J=22.0 Hz, 2H), 3.99-4.09 (m, 4H), 7.17 (m, 3H), 7.72 (d, J=7.5 Hz, 1H), 8.52 (s, 1H).

Prepared analogously to Compound 5E replacing Compound 5F with a mixture of 1-[3-(benzyloxy)propyl]-4-iodo-3-methyl-1H-pyrazole and 1-[3-(benzyloxy)propyl]-4-iodo-5-methyl-1H-pyrazole (Compound 34H and Compound 34I, 3.60 g, 10.1 mmol) to afford 5.8 g of the title compounds as a mixture of regioisomers (80%). MS (ESI): m/z=357.21 [M+H]+. UPLC: tR=1.67-1.69 min (UPLC-TOF: polar—3 min).

A mixture of 3-methyl-4-iodopyrazole (2.59 g, 12.5 mmol) and 1-bromo-3-benzyloxypropane (3.00 g, 13.1 mmol) in DMF (11.4 mL) was charged with potassium carbonate (2.07 g, 15.0 mmol). The reaction mixture was allowed to stir at rt for 16 hrs overnight. The reaction mixture was quenched with water and then extracted with EtOAc. The organic layer was washed with water, brine (2×), dried over sodium sulfate, filtered, and then concentrated in vacuo to yield an oil. The crude material was purified using a Teledyne ISCO Combiflash® Rf system [Heptane/EtOAc (100:0→0:100)] to afford the title products as a mixture of regioisomers (3.60 g, 41% combined yield). The reaction was carried onto the next step without any further purification. MS (ESI): m/z=357.02 [M+H]+. UPLC: tR=1.62 min (UPLC-TOF: polar—3 min).

Prepared analogously to Compound 1E replacing compound 1F with ethyl (4-amino-3-methoxybenzyl)propylphosphinate (Compound 37D, 0.971 g, 3.58 mmol). The crude material was purified on a Teledyne ISCO Combiflash® Rf system using DCM/MeOH (100:0→95:5) as eluent to afford the title compound as 1.08 g of a white foam (67%). MS (ESI): m/z 452.10 [M+H]+. UPLC: tR=1.10 min (polar—2 min).

A mixture of ammonium phosphinate (1.00 g, 12.0 mmol) and Hexamethyldisilazane (1.94 g, 12.0 mmol) was heated to 110° C. under N2for approximately 1.5 hours. The reaction mixture was cooled to 0° C., charged with anhydrous DCM (10 mL) followed by Allyl bromide (1.46 g, 12.0 mmol) and allowed to stir at RT for 16 hours. The reaction mixture was then cooled to 0° C. and charged with more hexamethyldisilazane (1.94 g, 12.0 mmol). The reaction mixture was stirred at 0° C. for 2 hours then treated with 4-(bromomethyl)-2-methoxy-1-nitrobenzene (3.00 g, 12.2 mmol). The reaction mixture was allowed to stir for 16 hours at rt after which it was filtered. The filtrate was quenched with 1N HCl (10 mL) and extracted with DCM (20 mL). The organic layer was washed with brine (10 mL), dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure to a yellow oil. The material was dissolved in DCM and extracted with aq. NaHCO3. The aqueous layer was cooled to 0° C. and then acidified with 6 M HCl. The aqueous layer was saturated with solid NaCl then extracted with DCM. The organic layer was concentrated under reduced pressure to a yellow oil (1.29 g, 39%). This material was used in successive reactions without any further purification.1H NMR (CDCl3, 400 MHz): δ=9.81 (br. s., 1H), 7.81 (d, J=8.3 Hz, 1H), 7.01 (s, 1H), 6.89 (td, J=1.8, 8.3 Hz, 1H), 5.79-5.67 (m, 1H), 5.29-5.18 (m, 2H), 3.96 (s, 3H), 3.10 (d, J=15.9 Hz, 2H), 2.53-2.44 (m, 2H). MS (ESI): m/z 270.37 [M−H]+. UPLC: tR=0.76 min (UPLC-SQD: analytical—2 min).

An ice cooled solution of (3-(benzyloxymethyl)oxetan-3-yl)methanol (Example 44E, 1.00 g, 4.80 mmol) in DCM (5.14 mL) was treated with triethylamine (1.31 mL, 9.43 mmol) and methanesulfonyl chloride (0.438 mL, 5.66 mmol) and gradually allowed to warm up to rt over 16 hrs. The mixture was diluted with DCM, washed with saturated aqueous NaHCO3solution (1×), brine (2×), dried over anhydrous sodium sulfate, filtered, concentrated in vacuo to a solid to afford 7.2 g of the title compound (100%). The crude product was used in next step without further purification.1H NMR (400 MHz, CD3OD) δ 7.23-7.38 (m, 5H), 4.58 (s, 2H), 4.46-4.54 (m, 6H), 3.74 (s, 2H), 3.09 (s, 3H).

A suspension of 3-amino-N-methoxypyridine-2-carboxamide (Compound 46E, 0.275 g, 1.64 mmol) in H2O (4.5 mL) was treated with a drop of Sulfuric acid and 0.6 mL of AcOH. After about 10 min of vigorous stirring, a solution of Bromine (84.7 uL, 1.64 mmol) in 0.4 mL of AcOH was cautiously added. After an additional 15-20 min of stirring the texture of the reaction mixture/suspension changed to become a more coarse orange ppt. This material was collected by filtration and dried to afford 240 mg of the title compound as an orange solid (59%).1H NMR (400 MHz, DMSO-d6) δ 11.51 (s, 1H), 7.40 (d, J=8.8 Hz, 1H), 7.14 (d, J=8.8 Hz, 1H), 6.91 (br. s., 2H), 3.66 (s, 3H); MS (ESI): m/z=245.98, 247.98 [M+H]+; UPLC: tR=0.67 min (UPLC-TOF: polar—2 min)

1-[2,2-dimethyl-3-(tetrahydro-2H-pyran-2-yloxy)propyl]-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole (Compound 47C, 539 mg, 1.48 mmol) was dissolved in EtOH (2.64 mL) and p-TsOH.H2O (56.3 mg, 0.296 mmol) was added to the reaction mixture. The reaction was left to stir at rt for 16 hrs. Solid NaHCO3(1.24 g, 14.8 mmol) was added to the reaction mixture and left to stir at rt for an additional 30 min. The reaction mixture was quenched with water and then extracted with EtOAc. The organic layer was washed with sat. NaHCO3(1×), brine (2×), extracted, dried over sodium sulfate, filtered, concentrated in vacuo and purified using a Teledyne ISCO Combiflash® Rf system [0-30% Acetone/Heptanes] to afford 237 mg of the title compound (57%). MS (ESI): m/z=281.38 [M+H]+. UPLC: tR=1.12 min (UPLC-TOF: polar—2 min).

A cold (−20° C.) solution of 3-(4-Iodopyrazol-1-yl)-2,2-dimethylpropionic acid methyl ester (Compound 47F, 6.0 g, 19.48 mmol) in THF (80 mL) was treated with DIBAL (42.85 mL, 42.85 mmol, 1M solution in toluene) and allowed to warm to RT over a period of 2 h. The reaction mixture was treated with aq. ammonium hydroxide (20 mL) and the solids were filtered through celite. The filtrate was diluted with ethyl acetate (50 mL) and washed with brine (2×50 mL). The organic layer was dried over Na2SO4, filtered and concentrated to give 4.9 g (90%) as an oil which crystallized upon standing.1H NMR (500 MHz, CDCl3) δ 7.50 (s, 1H), 7.41 (s, 1H), 4.0 (s, 2H), 3.17 (s, 3H), 0.9 (s, 6H).

A solution of 3-methoxy-1H-pyrazole (Compound 48G, 1.6 g, 16.32 mmol) in DMF (25 mL) was cooled to −30° C. and charged with NIS (3.67 g, 16.31 mmol). The reaction mixture was stirred at −30° C. for 1.5 h, and then H2O (30 mL) and EtOAc (40 mL) were added at −30° C. Organic layer was separated and the aqueous layer was re-extracted with EtOAc (3×20 mL) and the combined organic fractions were washed with H2O, 1M aqueous Na2S2O3, followed by brine, dried over Na2SO4, filtered and concentrated in vacuo to afford 2.1 g (58%) of the title compound as a light yellow solid. This material was taken on to the next step without further purification.1H NMR (300 MHz, CDCl3) δ 7.41 (s, 1H), 3.96 (s, 3H).

A solution of 1-acetyl-1,2-dihydro-3H-pyrazol-3-one (Molbank,2006 pp M464/1-M464/3, 3.0 g, 23.8 mmol), potassium carbonate (3.28 g, 23.8 mmol) in 2-butanone (72 mL) was charged with dimethyl sulfate (2.48 mL, 26.2 mmol) and heated to reflux for 90 min. The reaction mixture was cooled to rt, filtered and concentrated in vacuo to afford a dark yellow oil. The crude oil was taken up in 10 M aqueous NaOH (1.1 mL) and 80 mL of a 1:1 mixture of THF/MeOH and stirred at rt for 30 min and neutralized with 1N HCl. The reaction mixture was concentrated in vacuo and partitioned between EtOAc and brine (150 mL). The organic layer was dried over Na2SO4, filtered and concentrated in vacuo to afford 1.7 g (73%) of the title compound as an orange oil.1H NMR (300 MHz, CDCl3) δ 7.36 (d, J=2.7 Hz, 1H), 5.74 (d, J=2.4 Hz, 1H), 3.91 (s, 3H).

To a solution of diethyl 2-chloro-3-methoxy-4-nitrobenzylphosphonate (Compound 54F, 1 g, 2.96 mmol) in ethanol (15 mL), and iron powder (1.63 g, 29.6 mmol) was added aqueous 2N HCl (5 mL). The reaction mixture was heated to reflux for 1.5 h. The reaction mixture was cooled to RT and saturated solution of Na2CO3was added until the pH was 9. The reaction mixture was filtered through celite and concentrated to give the residue. It was dissolved in ethyl acetate (25 mL) and washed with water, dried over sodium sulfate, filtered and concentrated to give the required product (89%, 900 mg).1H NMR (300 MHz, CDCl3) δ 7.01 (d, 1H), 6.62 (d, 1H), 4.00-4.19 (m, 4H), 3.83 (s, 3H), 3.25 (d, 2H), 1.23 (t, 6H).

Potassium nitrate (4 g, 39.6 mmol) was added slowly to a solution of 2-chloro-3-hydroxybenzaldehyde (6 g, 35.2 mmol) in sulfuric acid (28 mL) at 30-40° C. The contents of the flasks were heated to 50-60° C. for 10 minutes and then poured onto ice (60 g). The solid obtained was steam distilled to provide the desired compound (1.6 g, 21%).1H NMR (300 MHz, CDCl3) δ 10.51 (s, 1H), 7.82-7.79 (m, 2H), 4.08 (s, 3H).

A suspension of (2-chloro-5-methoxy-4 nitrobenzyl)-phosphonic acid diethylester (Compound 56F, 10.3 g, 30.5 mmol), iron powder (16.8 g, 305 mmol) in 2M aqueous hydrochloric acid (25 mL) and ethanol (150 mL) was heated to reflux for 1 hr. The reaction mixture was cooled to RT and solid Na2CO3(6 g) was added until the pH was 9. The reaction mixture was filtered through celite, the filter cake was washed with dichloromethane and the filtrate was concentrated to give a residue which was dissolved in ethyl acetate, washed with water, dried over sodium sulfate, filtered and concentrated to give the required material as gum (8 g, 85%).1H NMR (400 MHz, CDCl3) δ: 6.88 (s, 1H), 6.71 (s, 1H), 4.3 (brs, 2H), 4.05-4.13 (m, 4H), 3.85 (s, 3H), 3.26 (d, J=20.50 Hz, 2H), 1.28 (t, J=7.05 Hz, 6H).

A mixture of 1-Bromomethyl-2-chloro-5-methoxy-4-nitro-benzene, 1-Chloro-4-methoxy-2-methyl-5-nitro-benzene and 1-chloro-2-dibromomethyl-4-methoxy-5-nitro-benzene (Compound 56G, 24 g, 1:015:0.5) in toluene (100 mL) were treated with triethylphosphite (15.6 g, 94.2 mmol) and heated to reflux for 24 hrs. Toluene and triethylphosphite were distilled off under reduced pressure. The residue was treated with hot diisopropyl ether to give 10 g of the required compound as dark yellow crystals.

A solution of 1-chloro-4-methoxy-2-methyl-5-nitro-benzene (13.2 g, 65.6 mmol) in dichloroethane (200 mL) was treated with N-bromosuccinimide (12.8 g, 72.2 mmol) and 1,1-azobis cyclohexane carbonitrile (0.5 g, 2 mmol). The reaction mixture was heated to reflux in presence of light for 24 hrs. The reaction mixture was then cooled to RT, washed with sodium thiosulfate (20% aq., 50 mL), water and brine. The organic layer was dried over magnesium sulfate, filtered and concentrated to give a residue (24 g) which by1H NMR was a mixture of desired product, starting material and the dibrominated product (1-chloro-2-dibromomethyl-4-methoxy-5-nitro-benzene) in a ratio of 1:0.5:0.15 and was carried to the next step without further purification.1H NMR (400 MHz, CDCl3) δ: 7.88 (s, 1H), 7.14 (s, 1H), 4.52 (s, 2H), 3.96 (s, 3H).

A solution of acetic acid 3-acetoxy-2-oxopropyl ester (6.2 g, 35.6 mmol) in DAST (11 mL) was stirred for 48 h. The reaction mixture was added to a mixture of ice and sat. sodium carbonate drop wise. The aq. layer was extracted with ethyl acetate (3×100 mL). The combined organic layers were dried over Na2SO4, filtered and concentrated to give 4.8 g (69%) of acetic acid 3-acetoxy-2,2-difluoro-propyl ester which was dissolved in methanol and treated with NaOMe (3.9 g, 73 mmol). After 6 h, the reaction mixture was neutralized with amberlite IR ion exchange resin (acidic). The resulting mixture was filtered and the filtrate was concentrated to 2.8 g (70%) of desired product as an oil.1H NMR (500 MHz, CDCl3) δ 3.91 (t, J=12.5 Hz, 4H), 1.8 (bs, 2H).

N-Bromosuccinimide (58.62 g, 329.34 mmol) was added in portions over a period of 5-10 min to a well stirred solution of 4-methyl-2-methoxy-1-nitro benzene (50.0 g, 299.4 mmol) and 1,1′-Azobis(cyclohexane carbonitrile) (1.0 g, 4.1 mmol) in dichloroethane (600 mL) and the resulting mixture was heated to reflux under a UV light for a maximum 7-8 hr. After cooling to rt, the reaction mixture was diluted with dichloromethane (400 mL) and washed with aqueous Na2S2O4solution, water and brine. The organic phase was dried over anhydrous Na2SO4, filtered and concentrated to give a crude solid (102.0 g) which was triturated with diisopropyl ether to afford 43.0 g of the desired product. The diisopropyl ether filtrate was concentrated and purified by silica-gel column chromatography (5-40% EtOAc/Hexanes) to obtain an additional 5.5 g of the desired product (48.5 g, 66%).1H NMR (CDCl3-300 MHz): δ=3.98 (s, 3H), 4.46 (s, 2H), 7.05 (dd, J=6.60 Hz, 1H), 7.10 (d, J=1.5 Hz, 1H), 7.82 (d, J=8.4 Hz, 1H).

A solution of −({1-[(benzyloxy)methyl]cyclopropyl}methyl)-4-(tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole (Compound 63C, 8 g, 21.7 mmol) in ethanol (100 mL) was treated with palladium on charcoal (10%, 6 g) and heated to 50° C. under hydrogen atmosphere for 24 hrs. The catalyst was filtered off and the filtrate was concentrated to a residue under reduced pressure. The residue was triturated with isopropyl ether to give 3.2 g (53%) of the required material as white solid.1H NMR (500 MHz, CDCl3) δ 7.81 (s, 1H), 7.7 (s, 1H), 4.14 (s, 2H), 3.38 (s, 2H), 1.33 (s, 12H), 0.54-0.65 (m, 4H).

Methane sulfonyl chloride (5.2 mL, 68.7 mmol) was added drop wise to an ice cooled solution of {1-[(benzyloxy)methyl]cyclopropyl}methanol (Compound 63E, 11 g, 57.2 mmol) and triethylamine (15.5 mL, 114 mmol) in dichloromethane (50 mL). The reaction mixture warmed to RT and allowed to stir overnight. The reaction mixture was filtered to remove solids. The filtrate was washed with saturated sodium bicarbonate solution followed by brine, dried over magnesium sulfate, filtered and concentrated to give 12 g (77%) of the desired product as light yellow oil which was used without further purification.1H NMR (400 MHz, CDCl3) δ 7.25-7.41 (m, 5H), 4.58 (s, 2H), 4.21 (s, 2H), 3.42 (s, 2H), 2.96 (s, 3H), 0.61-0.75 (m, 4H).

A solution of 5-bromo-2-{[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]amino}-N-methylbenzamide (Compound 66B, 150.5 mg, 0.3674 mmol) and 3-[4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazol-1-yl]propyl (4-amino-3-methoxybenzyl)propylphosphinate (Compound 66C, 175.4 mg, 0.3674 mmol) in TFE (5.0 mL) was charged with TFA (0.0602 mL). The reaction mixture was stirred at 50° C. for 24 hours. The reaction mixture was concentrated under reduced pressure to a light yellow oil and purified on a Teledyne ISCO Combiflash® Rf system using DCM/MeOH (100:0→90:10) as eluent to afford the racemic title compound as 0.245 g of a white solid (78%). MS (ESI): m/z 850.91/852.88 [M+H]+. UPLC: tR=1.52 min (UPLC-SQD: analytical—2 min).

A suspension of (4-{[4-{[6-bromo-2-(methylcarbamoyl)pyridin-3-yl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-3-methoxybenzyl)propan-2-ylphosphinic acid (Compound 68B, 0.240 g, 0.389 mmol) and 3-[4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazol-1-yl]propan-1-ol (Compound 3E, 97.9 g, 0.388 mmol) in 1,2-dichloroethane (8.53 mL) and DIPEA (0.812 mL, 4.66 mmol) was charged with (benzotriazol-1-yloxy)tripyrrolidino-phosphonium hexafluorophosphate (1.21 g, 2.33 mmol). The reaction mixture was stirred at 60° C. for 16 hours. The reaction mixture was quenched with water (10 mL) and extracted with DCM (20 mL). The organic layer was washed with NaHCO3(10 mL), washed with brine (15 mL), dried over anhydrous Na2SO4, filtered, and concentrated under reduced pressure to a brown oil. The crude material was purified using a Teledyne ISCO Combiflash® Rf system using 1:1 DCM-EtOAc/MeOH (100:0→90:10) as eluent to afford the title compound as an off-white foam. MS (ESI): m/z 851.84/853.82 [M+H]+. UPLC: tR=1.57 min (UPLC-SQD: analytical—2 min).

The reaction mixture was concentrated under reduced pressure to a black solid. The solid residue was dissolved in water (15 mL), then acidified with conc. HCl (pH ˜1-2) and extracted with DCM (20 mL). The organic layer was washed with water (15 mL), washed with brine (15 mL), dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure to a white solid (0.47 g, 90%). The material was used in successive reactions without any further purification. MS (ESI): m/z 633.50/635.54 [M+H]+. UPLC: tR=0.57 min (analytical—1 min).

A suspension of (4-{[4-{[6-bromo-2-(methylcarbamoyl)pyridin-3-yl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-3-methoxybenzyl)propylphosphinic acid (Compound 74B, 0.500 g, 0.810 mmol) and 2,2-dimethyl-3-[4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazol-1-yl]propan-1-ol (Compound 47B, 227 mg, 0.809 mmol) in 1,2-dichloroethane (24.4 mL) and 1-methylimidazole (0.967 mL, 12.1 mmol) was charged with (benzotriazol-1-yloxy)tripyrrolidino-phosphonium hexafluorophosphate (2530 mg, 4.85 mmol). After stirring at 60° C. for 16 hours, the reaction mixture was quenched with water (10 mL) and extracted with DCM (20 mL). The organic layer was washed with NaHCO3(10 mL), washed with brine (15 mL), dried over anhydrous Na2SO4, filtered, and concentrated under reduced pressure to a brown oil. The crude material was purified using a Teledyne ISCO Combiflash® Rf system using 1:1 DCM-EtOAc/MeOH (100:0→95:5) as eluent. The fractions containing product were combined and concentrated under reduced pressure to yield an off-white foam (318.1 mg, 45%). MS (ESI): m/z 879.93/881.94 [M+H]+. UPLC: tR=1.67 min (UPLC-TOF: polar—2 min).

SFC (Supercritical Fluid Chromatography) using a chiral stationary phase can be used to separate the preceding racemic Examples into the individual enantiomers. The following table lists each Example that was separated along with the relevant chiral SFC conditions used. With the exception of Examples 69 and 70, the1H NMR and LC-MS data for the enantiomers was identical to the data obtained for the racemic mixture:

In some aspects of the invention, compounds of the invention are inhibitors of kinases, including FAK. In some aspects of the invention, compounds of the invention are selective inhibitors of FAK.

The invention includes compounds that exhibit inhibition of FAK in a biochemical assay (such as described herein) with an IC50of about 1 μM or less, or about 100 nM or less, or about 10 nM or less.

The invention includes compounds that exhibit inhibition of FAK in a cellular assay (such as described herein) with an IC50of about 1 μM or less, or about 100 nM or less, or about 10 nM or less.

In some aspects of the invention, compounds of the invention are selective inhibitors of FAK. In some embodiments, a compound is a selective inhibitor of FAK over other kinase targets. In some embodiments, a compound is at least about 50-fold selective for FAK over Aurora B in a cellular assay. In some embodiments, a compound is at least about 1000-fold selective for FAK over Src and/or KDR in a cellular assay.

Compounds of the invention were evaluated in the following biochemical and mechanistic assays, results of which are shown in Table 1.

Biochemical Omnia Assay Protocol

The Omnia Assay (Invitrogen) has been optimized for GST-tagged full-length FAK enzyme (PTK2, Invitrogen PV4085). In this assay system, Omnia Y Peptide 3 (Invitrogen KNZ3031) functions as a substrate for FAK. Phosphorylation of this SOX-containing peptide by FAK results in an increase in fluorescence at 485 nm upon excitation at 360 nm. Assays were carried out in 384-well OptiPlates (Perkin Elmer 6007290) in a total volume of 20 μL containing FAK (25 nM), Omnia Y Peptide 3 (10 μM), ATP (50 μM), and test compound (variable) in assay buffer (50 mM HEPES, pH 7.5, 5 mM MgCl2, 0.15 mM MnCl2, 1% glycerol, 1 mM DTT, 1 mM EGTA, 0.01% BSA) with 1% DMSO.

IC50s for test compounds were typically determined using an 11-point three-fold serial dilution with a final assay concentration ranging from 0.17 nM to 10 μM. All compound concentrations were assayed in duplicate. Initial compound dilutions were prepared at 100× concentration in 100% DMSO from a 10 mM stock solution. Compounds were further diluted 1:25 in assay buffer resulting in a 4× concentrated solution.

In running the assay, 5 μL of the above 4× concentrated compound solution (or 4% DMSO for positive controls) was added to the assay plate followed by 5 μL of a solution containing peptide (40 μM) and ATP (200 μM) in assay buffer. The reaction was initiated by the addition of 10 μL of FAK (50 nM) in assay buffer, or assay buffer alone for negative controls. The increase in fluorescence due to peptide phosphorylation was monitored continuously as a function of time using a Spectramax M5 plate reader (Molecular Devices) equipped with SoftMax Pro 5.2 software.

IC50values were determined from the slopes of the linear progress curves by non-linear curve-fitting using GraphPad Prism 5 (GraphPad Software, Inc.). IC50's were determined in duplicate (n=2).

Cell-Based Assays for Inhibition of FAK Autophosphorylation: MiaPaCa2 and U87MG

The ability of compounds to inhibit FAK autophosphorylation was determined in a cell-based capture ELISA assay using U87MG glioblastoma cells (ATCC, Cat # HTB-14) and the FAK [pY397]ELISA kit from Invitrogen (KHO0441). The assay determines the ability of compounds to block endogenous autophosphorylation of FAK stimulated by fibronectin. Cells plated on fibronectin coated 96-well plate were incubated with compounds at various concentrations in the complete growth medium for 2 h. Cell lysates were then prepared and FAK protein was captured onto a FAK antibody-coated 96-well ELISA plate. The phosphotyrosine content of FAK protein was then monitored by quantitation of degree of binding of an antibody that recognizes only the phosphorylated FAK at Y397 within the captured protein. The antibody used has a reporter enzyme (e.g. horse radish peroxidase, HRP) covalently attached, such that binding to phosphorylated FAK can be determined quantitatively by incubation with an appropriate HRP substrate.

Cultures of U87MG cells growing in MEM (Earles) containing non-essential amino acids, sodium pyruvate (1 mM), L-glutamate (1%) and 10% fetal bovine serum were detached by trypsin-EDTA and suspended in cell growth medium. Cells were then plated onto fibronectin (600 ng/well)-coated 96-well flat bottom plates at 1.7×104cells per well in 60 uL cell growth medium and incubated overnight at 37° C. in a CO2incubator.

Compound dilutions were prepared from 10 mM DMSO stocks by dilution in cell growth medium, the final concentration of DMSO in the assay being 0.6%. To compound incubation wells, 60 uL of test compound was added as 2× concentration (compounds were assayed at concentrations between 4 μM-1.3 nM); to positive control wells, 60 μL of cell assay medium containing 1.3% DMSO was added. The cells were then incubated with compounds at 37° C. for 2 h. The medium was removed by aspiration and cells were lysed by addition of 20 uL of ice-cold cell lysis buffer per well. The plates were kept on ice for 20 min and 50 uL of standard diluent was added to each well. 50 uL of cell lysate from each well was transferred to respective wells in an assay plate and 50 uL of detection antibody was added to all wells except H1-H6 which were no antibody control wells. Capture assay plates were incubated overnight in a cold room.

Following incubation of the cell lysates and detection antibodies in the ELISA plate, the wells were washed 4 times with 120 uL of wash buffer (1×), then 100 uL of diluted HRP conjugated antibody (1:100 dil in diluent) was added to each well, and the plate was incubated at RT for 30 min. The wells were then washed for 4 times with 120 uL of wash buffer (1×) and 100 uL of chromogen was added to each well and incubated in the dark at RT for 5-10 min. 100 uL of stop solution was added to each well and the absorbance measured at 450 nm, 0.1 s.

Comparison of the assay signals obtained in the presence of compound with those of positive and negative controls (cells with no compound and no detection antibody being added), allows degree of inhibition of phospho-FAK [Y397] to be determined over a range of compound concentrations. These inhibition vales were fitted to a sigmoidal dose-response inhibition curve to determine the IC50values (i.e. the concentration of the compound that inhibits phosphorylation of FAK by 50%). The assay as described above was modified to determine the effect of inclusion of 50% (v/v) mouse or human plasma. In this assay, the compound plate was prepared as 2× concentration in 100 uL of 100% mouse or human plasma, and 60 uL of this was added to 60 uL of culture medium and incubated at 37° C. incubator for 2 h. The rest of the assay was carried out as described above.

In Table 2, A indicates a mean IC50of less than 0.4 μM; B indicates a mean IC50of 0.4 to 4 μM; and C indicates a mean IC50of greater than 4 μM. HP indicates assay in the presence of human plasma; MP indicates mouse plasma; NP indicates no plasma present.

The invention includes pharmaceutical compositions comprising a compound or pharmaceutically acceptable salt thereof of the invention, which is formulated for a desired mode of administration with or without one or more pharmaceutically acceptable and useful carriers. The compounds can also be included in pharmaceutical compositions in combination with one or more other therapeutically active compounds.

Compounds of the invention can be combined as the active ingredient in intimate admixture with a pharmaceutical carrier according to conventional pharmaceutical compounding techniques. The carrier can take a wide variety of forms depending on the form of preparation desired for administration, e.g., oral or parenteral (including intravenous). Thus, the pharmaceutical compositions of the present invention can be presented as discrete units suitable for oral administration such as capsules, cachets or tablets each containing a predetermined amount of the active ingredient. Further, the compositions can be presented as a powder, as granules, as a solution, as a suspension in an aqueous liquid, as a non-aqueous liquid, as an oil-in-water emulsion, or as a water-in-oil liquid emulsion. In addition to the common dosage forms set out above, the compound represented by Formula I, or a pharmaceutically acceptable salt thereof, can also be administered by controlled release means and/or delivery devices. The compositions can be prepared by any of the methods of pharmacy. In general, such methods include a step of bringing into association the active ingredient with the carrier that constitutes one or more necessary ingredients. In general, the compositions are prepared by uniformly and intimately admixing the active ingredient with liquid carriers or finely divided solid carriers or both. The product can then be conveniently shaped into the desired presentation.

A tablet containing the composition of this invention can be prepared by compression or molding, optionally with one or more accessory ingredients or adjuvants. Compressed tablets can be prepared by compressing, in a suitable machine, the active ingredient in a free-flowing form such as powder or granules, optionally mixed with a binder, lubricant, inert diluent, surface active or dispersing agent. Molded tablets can be made by molding in a suitable machine, a mixture of the powdered compound moistened with an inert liquid diluent. Each tablet preferably contains from about 0.05 mg to about 5 g of the active ingredient and each cachet or capsule preferably containing from about 0.05 mg to about 5 g of the active ingredient.

A formulation intended for the oral administration to humans may contain from about 0.5 mg to about 5 g of active agent, compounded with an appropriate and convenient amount of carrier material which may vary from about 5 to about 95 percent of the total composition. Unit dosage forms will generally contain between from about 1 mg to about 2 g of the active ingredient, typically 25 mg, 50 mg, 100 mg, 200 mg, 300 mg, 400 mg, 500 mg, 600 mg, 800 mg, or 1000 mg.

Compounds of the invention can be provided for formulation at high purity, for example at least about 90%, 95%, or 98% pure by weight.

Pharmaceutical compositions of the present invention can be in a form suitable for topical use such as, for example, an aerosol, cream, ointment, lotion, dusting powder, or the like. Further, the compositions can be in a form suitable for use in transdermal devices. These formulations may be prepared, utilizing a compound represented by Formula I of this invention, or a pharmaceutically acceptable salt thereof, via conventional processing methods. As an example, a cream or ointment is prepared by admixing hydrophilic material and water, together with about 5 wt % to about 10 wt % of the compound, to produce a cream or ointment having a desired consistency.

Uses and Methods

Compounds of the invention inhibit tyrosine kinase enzymes in animals, including humans, and may be useful in the treatment and/or prevention of various diseases and conditions such as hyperproliferative disorders, such as cancers. In particular, compounds of the invention, and compositions thereof, are inhibitors of FAK, and are useful in treating conditions modulated or driven, at least in part, by FAK, or for which inhibition of FAK is beneficial.

In some aspects, the invention includes a method of treating cancer comprising administering to a mammal in need thereof a therapeutically effective amount of a compound or salt of the invention.

A method of treating a cancer for which FAK inhibition is beneficial comprising administering to a mammal in need thereof a therapeutically effective amount of a compound or salt of the invention with or without one or more additional active agents.

In some aspects, the invention includes a method of treating a cancer mediated or driven at least in part by FAK comprising administering to a mammal in need thereof a therapeutically effective amount of a compound or salt of the invention.

In some aspects, the invention includes a method of treating or a method of manufacturing a medicament for treating a cancer, such as those above, which is mediated or driven at least in part by FAK, or for which inhibition of FAK is beneficial comprising administering to a mammal in need thereof a therapeutically effective amount of a compound or salt of the invention.

Compounds of the invention may be useful in the treatment of a variety of cancers, including, but not limited to, solid tumors, sarcoma, fibrosarcoma, osteoma, melanoma, retinoblastoma, rhabdomyosarcoma, glioblastoma, neuroblastoma, teratocarcinoma, hematopoietic malignancy, and malignant ascites. More specifically, the cancers include, but not limited to, lung cancer, bladder cancer, pancreatic cancer, kidney cancer, gastric cancer, breast cancer, colon cancer, prostate cancer (including bone metastases), hepatocellular carcinoma, ovarian cancer, esophageal squamous cell carcinoma, melanoma, an anaplastic large cell lymphoma, an inflammatory myofibroblastic tumor, and a glioblastoma.

In some aspects, the above methods are used to treat one or more of bladder, colorectal, nonsmall cell lung, breast, or pancreatic cancer. In some aspects, the above methods are used to treat one or more of ovarian, gastric, head and neck, prostate, hepatocellular, renal, glioma, or sarcoma cancer.

In some aspects, the invention includes a method, including the above methods, wherein the compound is used to inhibit cellular epithelial to mesenchymal transition (EMT).

In some embodiments, the method includes treatment with a compound of the invention as part of a regimen that includes administration of one or more additional active agents.

The invention includes practicing the methods of the invention in human patients, and alternatively, in non-human animals.

The invention includes selecting a compound of the invention and a method and treatment regimen according to the invention based on its physicochemical and biological properties.

The dosage strength and regimen will depend upon several variables appreciated by the skilled artisan. Generally, dosage levels on the order of from about 0.01 mg/kg to about 150 mg/kg of body weight per day, or about 0.1 mg/kg to about 10 mg/kg of body weight per day, may be useful or beneficial in the treatment of the above-indicated conditions, or about 0.5 mg to about 7 g per patient per day. For example, cancers may be treated by administration of from about 0.01 to 50 mg of the compound per kg body weight per day, or alternatively about 0.5 mg to about 3.5 g per day per patient.

It is understood, however, that the specific dose level for any particular patient will depend upon a variety of factors including the age, body weight, general health, sex, diet, time of administration, route of administration, rate of excretion, drug combination and the severity of the particular disease undergoing therapy.

As noted above, in some aspects, the method further comprises administering at least on additional active agent. In some aspects, the invention includes a method of treating cancer comprising administering to a mammal in need thereof a therapeutically effective amount of a compound or salt of the invention, wherein at least one additional active anti-cancer agent is used as part of the method. In some aspects, the invention includes a method of treating cancer mediated at least in part by FAK comprising administering to a mammal in need thereof a therapeutically effective regimen comprising a compound or salt of Formula I and at least one additional active agent.

GENERAL DEFINITIONS AND ABBREVIATIONS

Except where otherwise indicated, the following general conventions and definitions apply. Unless otherwise indicated herein, language and terms are to be given their broadest reasonable interpretation as understood by the skilled artisan. Any examples given are nonlimiting.

Any section headings or subheadings herein are for the reader's convenience and/or formal compliance and are non-limiting.

A recitation of a compound herein is open to and embraces any material or composition containing the recited compound (e.g., a composition containing a racemic mixture, tautomers, epimers, stereoisomers, impure mixtures, etc.). In that a salt, solvate, or hydrate, polymorph, or other complex of a compound includes the compound itself, a recitation of a compound embraces materials containing such forms. Isotopically labeled compounds are also encompassed except where specifically excluded. For example, hydrogen is not limited to hydrogen containing zero neutrons.

The compounds of the invention and term “compound” in the claims include any pharmaceutically acceptable salts or solvates, and any amorphous or crystal forms, or tautomers, whether or not specifically recited in context.

The term “active agent” of the invention means a compound of the invention in any salt, polymorph, crystal, solvate, or hydrated form.

The term “pharmaceutically acceptable salt(s)” is known in the art and includes salts of acidic or basic groups which can be present in the compounds and prepared or resulting from pharmaceutically acceptable bases or acids.

The term “substituted” and substitutions contained in formulas herein refer to the replacement of one or more hydrogen radicals in a given structure with a specified radical, or, if not specified, to the replacement with any chemically feasible radical. When more than one position in a given structure can be substituted with more than one substituent selected from specified groups, the substituents can be either the same or different at every position (independently selected) unless otherwise indicated. In some cases, two positions in a given structure can be substituted with one shared substituent. It is understood that chemically impossible or highly unstable configurations are not desired or intended, as the skilled artisan would appreciate. It is also to be understood that in the proper context a moiety may be a diradical or otherwise be multiply substituted. For example, the term “aryl” can include arylene, and “heteroaryl” can include heteroarylene groups, etc, when indicated as such.

In descriptions and claims where subject matter (e.g., substitution at a given molecular position) is recited as being selected from a group of possibilities, the recitation is specifically intended to include any subset of the recited group. In the case of multiple variable positions or substituents, any combination of group or variable subsets is also contemplated. Unless indicated otherwise, a substituent, diradical or other group referred to herein can be bonded through any suitable position to a referenced subject molecule. For example, the term “indolyl” includes 1-indolyl, 2-indolyl, 3-indolyl, etc.

Moreover, a listing of variables need not be mutually exclusive and such is not limiting. For example, “carbocyclic” includes phenyl. A recitation of “carbocyclic or phenyl” does not imply that the meaning of “carbocyclic” is limited or excludes phenyl.

The convention for describing the carbon content of certain moieties is “(Ca-b)” or “Ca-Cb” meaning that the moiety can contain any number of from “a” to “b” carbon atoms. C0alkyl means a single covalent chemical bond when it is a connecting moiety, and a hydrogen when it is a terminal moiety. Similarly, “x-y” can indicate a moiety containing from x to y atoms, e.g.,5-6heterocycloalkyl means a heterocycloalkyl having either five or six ring members. “Cx-y” may be used to define number of carbons in a group. For example, “C0-12alkyl” means alkyl having 0-12 carbons, wherein C0alkyl means a single covalent chemical bond when a linking group and means hydrogen when a terminal group.

The term “absent,” as used herein to describe a structural variable (e.g., “—R— is absent”) means that diradical R has no atoms, and merely represents a bond between other adjoining atoms, unless otherwise indicated.

Unless otherwise indicated (such as by a connecting “—”), the connections of compound name moieties are at the rightmost recited moiety. That is, the substituent name starts with a terminal moiety, continues with any bridging moieties, and ends with the connecting moiety. For example, “heteroarylthioC1-4alkyl is a heteroaryl group connected through a thio sulfur to a C1-4alkyl, which alkyl connects to the chemical species bearing the substituent.

The term “aliphatic” means any hydrocarbon moiety, and can contain linear, branched, and cyclic parts, and can be saturated or unsaturated.

The term “alkyl” means any saturated hydrocarbon group that is straight-chain or branched. Examples of alkyl groups include methyl, ethyl, propyl, 2-propyl, n-butyl, iso-butyl, tert-butyl, pentyl, and the like.

The term “alkenyl” means any ethylenically unsaturated straight-chain or branched hydrocarbon group. Representative examples include, but are not limited to, ethenyl, 1-propenyl, 2-propenyl, 1-, 2-, or 3-butenyl, and the like.

The term “alkynyl” means any acetylenically unsaturated straight-chain or branched hydrocarbon group. Representative examples include, but are not limited to, ethynyl, 1-propynyl, 2-propynyl, 1-, 2-, or 3-butynyl, and the like.

The term “alkoxy” means —O-alkyl, —O-alkenyl, or —O-alkynyl. “Haloalkoxy” means an —O-(haloalkyl) group. Representative examples include, but are not limited to, trifluoromethoxy, tribromomethoxy, and the like.

“Haloalkyl” means an alkyl, preferably lower alkyl, that is substituted with one or more same or different halo atoms.

“Hydroxyalkyl” means an alkyl, preferably lower alkyl, that is substituted with one, two, or three hydroxy groups; e.g., hydroxymethyl, 1 or 2-hydroxyethyl, 1,2-, 1,3-, or 2,3-dihydroxypropyl, and the like.

The term “alkanoyl” means —C(O)-alkyl, —C(O)-alkenyl, or —C(O)-alkynyl.

The term “cyclic” means any ring system with or without heteroatoms (N, O, or S(O)0-2), and which can be saturated or unsaturated. Ring systems can be bridged and can include fused rings. The size of ring systems may be described using terminology such as “x-ycyclic,” which means a cyclic ring system that can have from x to y ring atoms. For example, the term “9-10carbocyclic” means a 5, 6 or 6,6 fused bicyclic carbocyclic ring system which can be satd., unsatd. or aromatic. It also means a phenyl fused to one 5 or 6 membered satd. or unsatd. carbocyclic group. Nonlimiting examples of such groups include naphthyl, 1,2,3,4 tetrahydronaphthyl, indenyl, indanyl, and the like.

The term “carbocyclic” means a cyclic ring moiety containing only carbon atoms in the ring(s) without regard to aromaticity, including monocyclic, fused, and bridged systems. For example, a 3-10 membered carbocyclic means any chemically feasible ring systems having from 3 to 10 ring atoms.

The term “cycloalkyl” means a non-aromatic 3-12 carbocyclic mono-cyclic, bicyclic, or polycyclic aliphatic ring moiety. Cycloalkyl can be bicycloalkyl, polycycloalkyl, bridged, or spiroalkyl. One or more of the rings may contain one or more double bonds but none of the rings has a completely conjugated pi-electron system. Examples, without limitation, of cycloalkyl groups are cyclopropane, cyclobutane, cyclopentane, cyclopentene, cyclohexane, cyclohexadiene, adamantane, cycloheptane, cycloheptatriene, and the like.

The term “unsaturated carbocyclic” means any cycloalkyl containing at least one double or triple bond. The term “cycloalkenyl” means a cycloalkyl having at least one double bond in the ring moiety.

The terms “bicycloalkyl” and “polycycloalkyl” mean a structure consisting of two or more cycloalkyl moieties that have two or more atoms in common. If the cycloalkyl moieties have exactly two atoms in common they are said to be “fused”. Examples include, but are not limited to, bicyclo[3.1.0]hexyl, perhydronaphthyl, and the like. If the cycloalkyl moieties have more than two atoms in common they are said to be “bridged”. Examples include, but are not limited to, bicyclo[2.2.1]heptyl (“norbornyl”), bicyclo[2.2.2]octyl, and the like.

The term “spirocyclic” means a structure consisting of two cycloalkyl (optionally containing one or more heteroatoms) moieties that have exactly one atom in common.

The term “spiroalkyl” means a structure consisting of two cycloalkyl moieties that have exactly one atom in common. Examples include, but are not limited to, spiro[4.5]decyl, spiro[2.3]hexyl, and the like.

The term “aromatic” means a planar ring moieties containing 4n+2 pi electrons, wherein n is an integer.

The term “aryl” means an aromatic moieties containing only carbon atoms in its ring system. Non-limiting examples include phenyl, naphthyl, and anthracenyl. The terms “aryl-alkyl” or “arylalkyl” or “aralkyl” refer to any alkyl that forms a bridging portion with a terminal aryl.

“Aralkyl” means alkyl, preferably lower alkyl, that is substituted with an aryl group as defined above; e.g., —CH2phenyl, —(CH2)2phenyl, —(CH2)3phenyl, CH3CH(CH3)CH2phenyl, and the like and derivatives thereof.

The term “heterocyclic” means a cyclic ring moiety containing at least one heteroatom (N, O, or S(O)0-2), including heteroaryl, heterocycloalkyl, including unsaturated heterocyclic rings.

The term “heterocycloalkyl” means a non-aromatic monocyclic, bicyclic, or polycyclic heterocyclic ring moiety of 3 to 12 ring atoms containing at least one ring having one or more heteroatoms. The rings may also have one or more double bonds. However, the rings do not have a completely conjugated pi-electron system. Examples of heterocycloalkyl rings include azetidine, oxetane, tetrahydrofuran, tetrahydropyran, oxepane, oxocane, thietane, thiazolidine, oxazolidine, oxazetidine, pyrazolidine, isoxazolidine, isothiazolidine, tetrahydrothiophene, tetrahydrothiopyran, thiepane, thiocane, azetidine, pyrrolidine, piperidine, N-methylpiperidine, azepane, 1,4-diazapane, azocane, [1,3]dioxane, oxazolidine, piperazine, homopiperazine, morpholine, thiomorpholine, 1,2,3,6-tetrahydropyridine and the like. Other examples of heterocycloalkyl rings include the oxidized forms of the sulfur-containing rings. Thus, tetrahydrothiophene-1-oxide, tetrahydrothiophene-1,1-dioxide, thiomorpholine-1-oxide, thiomorpholine-1,1-dioxide, tetrahydrothiopyran-1-oxide, tetrahydrothiopyran-1,1-dioxide, thiazolidine-1-oxide, and thiazolidine-1,1-dioxide are also considered to be heterocycloalkyl rings. The term “heterocycloalkyl” also includes fused ring systems and can include a carbocyclic ring that is partially or fully unsaturated, such as a benzene ring, to form benzofused heterocycloalkyl rings. For example, 3,4-dihydro-1,4-benzodioxine, tetrahydroquinoline, tetrahydroisoquinoline and the like. The term “heterocycloalkyl” also includes heterobicycloalkyl, heteropolycycloalkyl, or heterospiroalkyl, which are bicycloalkyl, polycycloalkyl, or spiroalkyl, in which one or more carbon atom(s) are replaced by one or more heteroatoms selected from O, N, and S. For example, 2-oxa-spiro[3.3]heptane, 2,7-diaza-spiro[4.5]decane, 6-oxa-2-thia-spiro[3.4]octane, octahydropyrrolo[1,2-a]pyrazine, 7-azabicyclo[2.2.1]heptane, 2-oxa-bicyclo[2.2.2]octane, and the like, are such heterocycloalkyls.

Non-aryl heterocyclic groups include satd. and unsatd. systems and can include groups having only 4 atoms in their ring system. The heterocyclic groups include benzo-fused ring systems and ring systems substituted with one or more oxo moieties. Recitation of ring sulfur is understood to include the sulfide, sulfoxide or sulfone where feasible. The heterocyclic groups also include partially unsatd. or fully satd. 4-10 membered ring systems, e.g., single rings of 4 to 8 atoms in size and bicyclic ring systems, including aromatic 6-membered aryl or heteroaryl rings fused to a non-aromatic ring. Also included are 4-6 membered ring systems (“4-6 membered heterocyclic”), which include 5-6 membered heteroaryls, and include groups such as azetidinyl and piperidinyl. Heterocyclics can be heteroatom-attached where such is possible. For instance, a group derived from pyrrole can be pyrrol-1-yl (N-attached) or pyrrol-3-yl (C-attached). Other heterocyclics include imidazo[4,5-b]pyridin-3-yl and benzoimidazol-1-yl.

The term “unsaturated heterocyclic” means a heterocycloalkyl containing at least one unsaturated bond. The term “heterobicycloalkyl” means a bicycloalkyl structure in which at least one carbon atom is replaced with a heteroatom. The term “heterospiroalkyl” means a spiroalkyl structure in which at least one carbon atom is replaced with a heteroatom.

Examples of partially unsaturated heteroalicyclic groups include, but are not limited to 3,4-dihydro-2H-pyranyl, 5,6-dihydro-2H-pyranyl, 2H-pyranyl, 1,2,3,4-tetrahydropyridinyl, and 1,2,5,6-tetrahydropyridinyl.

The terms “heteroaryl” or “hetaryl” mean a monocyclic, bicyclic, or polycyclic aromatic heterocyclic ring moiety containing 5-12 atoms. Examples of such heteroaryl rings include, but are not limited to, furyl, thienyl, pyrrolyl, pyrazolyl, imidazolyl, oxazolyl, isoxazolyl, thiazolyl, isothiazolyl, triazolyl, oxadiazolyl, thiadiazolyl, tetrazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, and triazinyl. The terms “heteroaryl” also include heteroaryl rings with fused carbocyclic ring systems that are partially or fully unsaturated, such as a benzene ring, to form a benzofused heteroaryl. For example, benzimidazole, benzoxazole, benzothiazole, benzofuran, quinoline, isoquinoline, quinoxaline, and the like. Furthermore, the terms “heteroaryl” include fused 5-6, 5-5, 6-6 ring systems, optionally possessing one nitrogen atom at a ring junction. Examples of such hetaryl rings include, but are not limited to, pyrrolopyrimidinyl, imidazo[1,2-a]pyridinyl, imidazo[2,1-b]thiazolyl, imidazo[4,5-b]pyridine, pyrrolo[2,1-f][1,2,4]triazinyl, and the like. Heteroaryl groups may be attached to other groups through their carbon atoms or the heteroatom(s), if applicable. For example, pyrrole may be connected at the nitrogen atom or at any of the carbon atoms.

“Heteroaralkyl” group means alkyl, preferably lower alkyl, that is substituted with a heteroaryl group; e.g., —CH2pyridinyl, —(CH2)2pyrimidinyl, —(CH2)3imidazolyl, and the like, and derivatives thereof.

A pharmaceutically acceptable heteroaryl is one that is sufficiently stable to be attached to a compound of the invention, formulated into a pharmaceutical composition and subsequently administered to a patient in need thereof.

“Arylthio” means an —S-aryl or an —S-heteroaryl group, as defined herein. Representative examples include, but are not limited to, phenylthio, pyridinylthio, furanylthio, thienylthio, pyrimidinylthio, and the like and derivatives thereof.

“Aryloxy” means an —O-aryl or an —O-heteroaryl group, as defined herein. Representative examples include, but are not limited to, phenoxy, pyridinyloxy, furanyloxy, thienyloxy, pyrimidinyloxy, pyrazinyloxy, and the like, and derivatives thereof.

One in the art understands that an “oxo” requires a second bond from the atom to which the oxo is attached. Accordingly, it is understood that oxo cannot be substituted onto an aryl or heteroaryl ring.

“Acyl” means a —C(O)R group, where R can be selected from the nonlimiting group of hydrogen or optionally substituted lower alkyl, trihalomethyl, unsubstituted cycloalkyl, aryl. “Thioacyl” or “thiocarbonyl” means a—C(S)R″ group, with R as defined above.

The term “protecting group” means a suitable chemical group that can be attached to a functional group and removed at a later stage to reveal the intact functional group. Examples of suitable protecting groups for various functional groups are described in T. W. Greene and P. G. M. Wuts, Protective Groups in Organic Synthesis, 2d Ed., John Wiley and Sons (1991 and later editions); L. Fieser and M. Fieser, Fieser and Fieser's Reagents for Organic Synthesis, John Wiley and Sons (1994); and L. Paquette, ed. Encyclopedia of Reagents for Organic Synthesis, John Wiley and Sons (1995). The term “hydroxy protecting group”, as used herein, unless otherwise indicated, includes Ac, CBZ, and various hydroxy protecting groups familiar to those skilled in the art including the groups referred to in Greene.

As used herein, the term “pharmaceutically acceptable salt” means those salts which retain the biological effectiveness and properties of the parent compound and do not present insurmountable safety or toxicity issues.

The term “pharmaceutical composition” means an active compound in any form suitable for effective administration to a subject, e.g., a mixture of the compound and at least one pharmaceutically acceptable carrier.

As used herein, a “physiologically/pharmaceutically acceptable carrier” means a carrier or diluent that does not cause significant irritation to an organism and does not abrogate the biological activity and properties of the administered compound.

The terms “treat,” “treatment,” and “treating” means reversing, alleviating, inhibiting the progress of, or partially or completely preventing the disorder or condition to which such term applies, or one or more symptoms of such disorder or condition. “Preventing” means treating before an infection occurs.

“Therapeutically effective amount” means that amount of the compound being administered which will relieve to some extent one or more of the symptoms of the disorder being treated, or result in inhibition of the progress or at least partial reversal of the condition.