NZ716281B2 - Aryl ethers and uses thereof - Google Patents

Abstract

The present disclosure relates to HIF-2? inhibitors and methods of making and using them for treating cancer. Certain compounds were potent in HIF-2? scintillation proximity assay, luciferase assay, and VEGF ELISA assay, and led to tumor size reduction and regression in 786-O xenograft bearing mice in vivo. in vivo.

Description

(12) Granted patent specificaon (19) NZ (11) 716281 (13) B2 (47) Publicaon date: 2021.12.24 (54) ARYL ETHERS AND USES THEREOF (51) Internaonal Patent Classificaon(s): A61K 31/085 C07D 213/89 A61K 31/44 C07C 13/45 A61P 35/00 (22) Filing date: (73) Owner(s): 2014.09.05 PELOTON THERAPEUTICS, INC. (23) Complete specificaon filing date: (74) Contact: 2014.09.05 AJ PARK (30) Internaonal Priority Data: (72) Inventor(s): US 61/978,421 2014.04.11 WALLACE, Eli, M.

US 61/875,674 2013.09.09 DIXON, Darryl, David GRINA, Jonas (86) Internaonal Applicaon No.: JOSEY, John, A.

RIZZI, James, P.

SCHLACHTER, Stephen, T. (87) Internaonal Publicaon number: WANG, Bin WO/2015/035223 WEHN, Paul XU, Rui YANG, Hanbiao (57) Abstract: The present disclosure relates to HIF-2α inhibitors and methods of making and using them for treang cancer. Certain compounds were potent in HIF-2α scinllaon proximity assay, luciferase assay, and VEGF ELISA assay, and led to tumor size reducon and regression in 786-O xenogra bearing mice in vivo.

NZ 716281 B2 ARYL ETHERS AND USES THEREOF This invention was in part funded by a grant from Cancer Prevention Research Institute of Texas (Grant number R1009).

The present application claims benefit of priority to U.S. Provisional Application Serial Nos. 61/875,674, filed September 9, 2013, and 61/978,421, filed April 11, 2014, the entire contents of each application being hereby incorporated by reference.

Intratumoral hypoxia is a driving force in cancer progression and is closely linked to poor patient prognosis and resistance to chemotherapy and radiation treatment.

Progress over the past several decades in mapping the molecular mechanisms that enable cellular adaptation to chronic oxygen deprivation has intensified interest in identifying drugs that effectively block the hypoxic response pathway in tumors. Hypoxia-Inducible Factors (HIF-1α and HIF-2α) are transcription factors that play central roles in this pathway, and thus represent attractive targets for therapeutic intervention. The half-life of HIF-α proteins is tightly regulated by the oxidative status within the cell. Under normoxic conditions, specific proline residues on the HIF proteins are hydroxylated by the oxygen sensitive HIF-specific prolyl-hydroxylases (PHD). The tumor suppressor von Hippel-Lindau (VHL) protein binds to the specific hydroxylated proline residues and recruits E3 ubiquition-ligase complex that targets HIF-α proteins for proteasomal degradation. Because PHDs require oxygen to function, under hypoxic conditions, HIF-α proteins accumulate and enter the nucleus to activate gene expression. Genetic mutations of the VHL gene that result in loss of function lead to constitutively active HIF-α proteins regardless of oxygen levels. Upon activation, these transcription factors stimulate the expression of genes that coordinately regulate anaerobic metabolism, angiogenesis, cell proliferation, cell survival, extracellular matrix remodeling, pH homeostasis, amino acid and nucleotide metabolism, and genomic instability.

While many gene products involved in the hypoxic response have been explored individually as therapeutic targets for cancer, broad inhibition of the pathway through direct targeting of HIF-α proteins offers an exciting opportunity to attack tumors on multiple fronts (Keith, et al.

Nature Rev. Cancer 12: 9-22, 2012).

Both HIF-1α and HIF-2α form a dimeric complex with HIF-1β (or ARNT: aryl hydrocarbon receptor nuclear translocator) and subsequently bind to hypoxia response elements (HRE) in target genes. Because the level of HIF-1β is unaffected by oxygen levels or VHL, transcriptional activity of the complex is largely driven by the availability of the HIF-α proteins. While HIF-1α and HIF-2α share significant sequence homology, they differ in tissue distribution, sensitivity to hypoxia, timing of activation and target gene specificity (Hu, et al. Mol. Cell Biol. 23: 9361-9374, 2003 and Keith, et al. Nature Rev. Cancer 12: 9-22, 2012). Whereas HIF-1α mRNA is ubiquitously expressed, the expression of HIF-2α mRNA is found primarily in kidney fibroblasts, hepatocytes and intestinal lumen epithelial cells.

Consistent with the tight regulation of the HIF-α proteins under normal physiology, neither is detected in normal tissue with the exception of HIF-2α in macrophages (Talks, et al. Am. J.

Pathol. 157: 411-421, 2000). However, HIF-2α protein has been detected in various human tumors of the bladder, breast, colon, liver, ovaries, pancreas, prostate and kidney as well as tumor-associated macrophages (Talks, et al. Am. J. Pathol. 157: 411-421, 2000). HIF-1α has been reported to give a transient, acute transcriptional response to hypoxia while HIF-2α provides more prolonged transcriptional activity. Furthermore, HIF-2α has greater transcriptional activity than HIF-1α under moderately hypoxic conditions like those encountered in end capillaries (Holmquist-Mengelbier, et al. Cancer Cell 10: 413-423, 2006).

Whereas some hypoxia-regulated genes are controlled by both HIF-1α and HIF-2α, some are only responsive to specific HIF-α proteins. For example, lactate dehydrogenase A (LDHA), phosphoglycerate kinase (PGK) and pyruvate dehydrogenase kinase 1 (PDK1) are uniquely controlled by HIF-1α whereas Oct-4 and erythropoietin (EPO) by HIF-2α. Often the relative contributions of the HIF-α proteins to gene transcription are cell type-, and disease-specific.

More importantly, the HIF-α proteins may play contrasting roles in tumorigenesis. For example, the oncogene MYC is a transcription factor that controls cell cycle G1/S transition.

MYC is overexpressed in 40% of human cancer. It has been shown that HIF-2α activity increases MYC transcription activity whereas HIF-1α inhibits MYC activity. As a result, in MYC driven tumors, HIF-2α inhibition reduced proliferation whereas HIF-1α inhibition increased growth (Gordan, et al. Cancer Cell 11: 335-347, 2007 and Koshiji et al. EMBO J. 23: 1949-1956, 2004).

Therefore, the identification of effective small molecules to modulate the activity of HIF-2α is desirable. [005a] In this specification where reference has been made to patent specifications, other external documents, or other sources of information, this is generally for the purpose of providing a context for discussing the features of the invention. Unless specifically stated otherwise, reference to such external documents is not to be construed as an admission that such documents, or such sources of information, in any jurisdiction, are prior art, or form part of the common general knowledge in the art. [005b] The invention is defined in the claims. However, the disclosure preceding the claims may refer to additional methods and other subject matter outside the scope of the present claims. This disclosure is retained for technical purposes.

Summary [005c] In a first aspect, the invention provides a compound of Formula III: (R ) n III, or a pharmaceutically acceptable salt thereof, wherein: R is phenyl or pyridyl, wherein said phenyl or pyridyl is substituted with at least one substituent selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano; R4 is selected from the group consisting of CN, -CF3, -S(=O)CH3, -S(=O) CH , -S(=O) CH F, -S(=O) CHF , -S(=O) CF , -S(=O) NH , -S(=O) NHCH , 2 3 2 2 2 2 2 3 2 2 2 3 -S(=O)(=NH)CH3, -S(=O)(=NH)CH2F, -S(=O)(=NH)CHF2, -S(=O)(=NH)CF3, -S(=O)(=N-CN)CH , -S(=O)(=N-CN)CH F, -S(=O)(=N-CN)CHF , and 3 2 2 -S(=O)(=N-CN)CF3; n is 1, 2, 3 or 4; R is hydrogen, hydroxy, alkoxy or amino; R is hydrogen, alkyl, alkenyl or alkynyl, or R and R in combination form 9 8 9 oxo; and each of R is independently selected from the group consisting of fluoro, hydroxy, alkyl, and heteroalkyl, with the proviso that when R is hydroxy, n is 1 or 2. [005d] In a second aspect, the invention provides a of Formula IV: or a pharmaceutically acceptable salt thereof, wherein: R is phenyl or pyridyl, wherein said phenyl or pyridyl is optionally substituted with one or more substituents selected from the group consisting of halo, alkyl, alkoxy, and cyano; R is selected from the group consisting of -CN, -CF , -S(=O)CH , -S(=O) CH , -S(=O) CH F, -S(=O) CHF , -S(=O) CF , -S(=O) NH , 2 3 2 2 2 2 2 3 2 2 -S(=O) NHCH , -S(=O)(=NH)CH , -S(=O)(=NH)CH F, -S(=O)(=NH)CHF , 2 3 3 2 2 -S(=O)(=NH)CF , -S(=O)(=N-CN)CH , -S(=O)(=N-CN)CH F, 3 3 2 -S(=O)(=N-CN)CHF , and-S(=O)(=N-CN)CF ; and R is hydroxy or amino. [005e] In a third aspect, the invention provides a compound of Formula Vd: or a pharmaceutically acceptable salt thereof, wherein: R is phenyl or pyridyl, wherein said phenyl or pyridyl is substituted with at least one substituent selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano; R is selected from the group consisiting of –CN, –CF , –S(=O)CH , 4 3 3 –S(=O) CH , –S(=O) CH F, –S(=O) CHF , –S(=O) CF , –S(=O) NH , 2 3 2 2 2 2 2 3 2 2 –S(=O) NHCH , –S(=O)(=NH)CH , –S(=O)(=NH)CH F, –S(=O)(=NH)CHF , 2 3 3 2 2 –S(=O)(=NH)CF , –S(=O)(=N-CN)CH , –S(=O)(=N-CN)CH F, –S(=O)(=N- 3 3 2 CN)CHF , and –S(=O)(=N-CN); R is hydrogen, halo or alkyl; and R is hydroxy, alkylamino, alkoxy or amino. [005f] In a fourth aspect, the invention provides a compound of Formula Vb: or a pharmaceutically acceptable salt thereof, wherein: R is phenyl or pyridyl, wherein said phenyl or pyridyl is substituted with at least one substituent selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano; R is selected from the group consisting of –CN, –CF , –S(=O)CH , 4 3 3 –S(=O) CH , –S(=O) CH F, –S(=O) CHF , –S(=O) CF , –S(=O) NH , 2 3 2 2 2 2 2 3 2 2 –S(=O) NHCH , –S(=O)(=NH)CH , –S(=O)(=NH)CH F, –S(=O)(=NH)CHF , 2 3 3 2 2 –S(=O)(=NH)CF , –S(=O)(=N-CN)CH , –S(=O)(=N-CN)CH F, –S(=O)(=N- 3 3 2 CN)CHF , and –S(=O)(=N-CN)CF R is hydrogen, halo or alkyl; and R is hydroxy, alkylamino, alkoxy or amino. [005g] In fifth aspect, the invention provides a pharmaceutical composition comprising a therapeutically effective amount of a compound or pharmaceutically acceptable salt according to any of the first to fourth aspects and a pharmaceutically acceptable carrier. [005h] In sixth aspect, the invention relates to use of a compound according to any of the first to fourth aspects in the manufacture of a medicament for the treatment of von Hippel-Lindau (VHL) disease. [005i] In sixth aspect, the invention relates to use of a compound according to any of the first to fourth aspects in the manufacture of a medicament for the treatment of renal cell carcinoma.

Described herein is a compound of Formula I or a pharmaceutically acceptable salt thereof, wherein: R is aryl or heteroaryl; R is nitro, carboxaldehyde, carboxylic acid, ester, amido, cyano, halo, sulfonyl, alkyl or heteroalkyl; R is hydrogen, halo, cyano, alkyl, heteroalkyl, alkenyl, alkynyl, alkylamino, carboxaldehyde, carboxylic acid, oxime, ester, amido or acyl, or R /R and atoms they are attached to form a 5- or 6- membered carbocycle with at least one sp hybridized carbon; R is nitro, halo, cyano, alkyl, sulfinyl, sulfonamide, sulfonyl or sulfoximinyl; and R is hydrogen, halo or alkyl.

In another aspect, the present disclosure provides a pharmaceutical composition comprising a compound described herein and a pharmaceutically acceptable carrier or excipient. The compound may exist in an amorphous form, a crystalline form, or as a salt, solvate or hydrate.

Described herein is a method of treating renal cell carcinoma by administrating a therapeutically effective amount of a compound described herein or a pharmaceutical composition thereof to a subject in need of such treatment. In some embodiments, the subject is a human.

Described herein is a method of inhibiting the activities of HIF-2α in a cell, comprising contacting the cell with an effective amount of a compound described herein.

Described herein is a kit comprising a pharmaceutical composition comprising a compound described herein and a pharmaceutically acceptable carrier or excipient and an instruction for using the composition to treat a subject suffering from cancer. In some embodiments, the cancer is renal cell carcinoma.

Brief Description of Figures Figure 1 shows treatment of renal cell carcinoma 786-O xenograft bearing mice at 0 mg/kg (denoted as “Veh”), 10 mg/kg, 30 mg/kg, and 100 mg/kg of Compound 15 three times each at 12 hour intervals. Figure 1 shows that Compound 15 treatment of renal cell carcinoma 786-O xenograft bearing mice reduced the mRNA levels of HIF-2α and HIF- 2α-regulated genes (PAI-1, CCND1, VEGFA, and GLUT1) in tumor. Compound 15 had no significant effect on the mRNA level of HIF-1α or non-HIF-2α-regulated genes (PGK1 and PDK1).

Figure 2 shows treatment of renal cell carcinoma 786-O xenograft bearing mice at 0 mg/kg (denoted as “Vehicle”) and 10 mg/kg of Compound 163 three times each at 12 hour intervals. Figure 2 shows that Compound 163 treatment of renal cell carcinoma 786-O xenograft bearing mice reduced the mRNA levels of HIF-2α and HIF-2α-regulated genes (PAI-1 and CCND1) in tumor. Compound 163 had no significant effect on the mRNA levels of HIF-1α and non-HIF-2α-regulated genes (PGK1 and PDK1).

Figure 3 shows treatment of 786-O xenograft bearing mice at 0 mg/kg (denoted as “Veh”), 10 mg/kg, 30 mg/kg, and 100 mg/kg of Compound 15 three times each at 12 hour intervals. Figure 3 shows that Compound 15 treatment of 786-O xenograft bearing mice reduced HIF-2α-regulated EPO gene expression in mouse kidney, but had no significant effect on the expression of HIF-1α-regulated PGK1 gene.

Figure 4 shows treatment of 786-O xenograft bearing mice at 0 mg/kg (denoted as “Veh”), 10 mg/kg, 30 mg/kg, and 100 mg/kg of Compound 15 three times each at 12 hour intervals. Figure 4 shows that Compound 15 treatment of 786-O xenograft bearing mice reduced the levels of HIF-2α and CyclinD1 proteins in tumor.

Figure 5 shows human VEGF levels of 786-O xenograft bearing mice before (denoted as “Prior to treatment”) and after treatment (denoted as “12h post treatment”) at 0 mg/kg (denoted as “Vehicle”), 10 mg/kg, 30 mg/kg, and 100 mg/kg of Compound 15 three times each at 12 hour intervals. Figure 5 shows that Compound 15 treatment of 786-O xenograft bearing mice reduced the plasma level of human VEGFA.

Figure 6 shows treatment of 786-O xenograft bearing mice at 0 mg/kg (denoted as “Vehicle”) and 10 mg/kg of Compound 163 three times each at 12 hour intervals. Figure 6 shows that Compound 163 treatment of 786-O xenograft bearing mice reduced the plasma level of human VEGFA.

Figure 7 shows treatment of 786-O xenograft bearing mice at 0 mg/kg (denoted as “Vehicle”), 3 mg/kg, 10 mg/kg, 30 mg/kg, and 100 mg/kg of Compound 15 BID and 40 mg/kg of sutent QD, respectively, for 20 days. Figure 7 shows that Compound 15 treatment of 786-O xenograft bearing mice as a single agent led to tumor size reduction and regression.

Figure 8 shows that Compound 163 treatment of 786-O xenograft bearing mice at 0 mg/kg (denoted as “Vehicle”) and 10 mg/kg BID of Compound 163 BID for 28 days. Figure 8 shows that Compound 163 treatment of 786-O xenograft bearing mice as a single agent led to tumor size reduction and regression.

Detailed Description of the Invention For purposes of interpreting this disclosure, the following definitions will apply.

The term "HIF-2α" refers to a monomeric protein that contains several conserved structured domains: basic helix-loop-helix (bHLH), and two Per-ARNT-Sim (PAS) domains designated PAS-A and PAS-B, in addition to C-terminal regulatory regions.

"HIF-2α" is also alternatively known by several other names in the scientific literature, including Endothelial PAS Domain Protein 1 (EPAS1), HIF2A, PASD2, HIFAlpha, HIF2- Alpha, HLF, Hypoxia-Inducible Factor 2-Alpha, HIF-1alpha-Like Factor, and MOP2. As a member of the bHLH/PAS family of transcription factors, "HIF-2α" forms an active heterodimeric transcription factor complex by binding to the ARNT (also known as HIF-1β) protein through non-covalent interactions.

The term “subject” includes, but is not limited to, humans of any age group, e.g., a pediatric subject (e.g., infant, child or adolescent) or adult subject (e.g., young adult, middle-aged adult or senior adult)) and/or other primates (e.g., cynomolgus monkeys or rhesus monkeys); mammals, including commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs; and/or birds, including commercially relevant birds such as chickens, ducks, geese, quail, and/or turkeys.

The term “scintillation proximity assay” (SPA) refers to a homogenous assay in which light is emitted when a radiolabeled ligand is brought into close proximity to a radiosensitive bead. The assay typically contains a target protein that contains a tag (e.g., His Tag, Glutathione S-transferase Tag). The tag on the protein is used to bind the target protein to the scintillation bead. Radio-labeled ligand (e.g., labeled with tritium) that binds to the protein is now in close proximity to the bead, and when the radio-label (e.g., tritium) decays, the high energy particle hits the bead resulting in the emission of light that is detected by a detector, such as photomultiplier tube or CCD camera. When unlabeled ligands or compounds that bind to the protein are used in the assay, they displace the radio-labeled ligand, resulting in loss of signal. For a general reference describing the assay, see Park, et al.

Analytical Biochemistry 269: 94-104, 1999.

HIF-2α activity as used herein has its ordinary meaning in the art. HIF-2α activity, for example, includes activation of gene transcription mediated by HIF-2α.

The term “inhibiting HIF-2α activity”, as used herein, refers to slowing, reducing, altering, as well as completely eliminating and/or preventing HIF-2α activity.

As used herein, the terms “treatment”, “treating”, “palliating” and “ameliorating” are used interchangeably herein. These terms refer to an approach for obtaining beneficial or desired results including, but are not limited to, therapeutic benefit and/or a prophylactic benefit. By therapeutic benefit is meant eradication or amelioration of the underlying disorder being treated. Also, a therapeutic benefit is achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the patient, notwithstanding that the patient can still be afflicted with the underlying disorder. For prophylactic benefit, the pharmaceutical compositions can be administered to a patient at risk of developing a particular disease, or to a patient reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.

The term “alkyl” refers to a straight or branched hydrocarbon chain radical comprising carbon and hydrogen atoms, containing no unsaturation, and having from one to ten carbon atoms (i.e., C1-C10 alkyl). Whenever it appears herein, a numerical range such as “1 to 10” refers to each integer in the given range; e.g., “1 to 10 carbon atoms” means that the alkyl group may consist of 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc., up to and including 10 carbon atoms, although the present definition also covers the occurrence of the term “alkyl” where no numerical range is designated. In some embodiments, it is a C1-C4 alkyl group. Typical alkyl groups include, but are in no way limited to, methyl, ethyl, n- propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, neopentyl, hexyl, septyl, and the like. The alkyl is attached to the rest of the molecule by a single bond. Unless stated otherwise specifically in the specification, an alkyl group is optionally substituted by one or more of the following substituents: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, cyano, nitro, oxo, thioxo, trimethylsilanyl, a a a a a a a —OR , —SR , —OC(=O)—R , —OC(=O)OR , —OC(=O)N(R ) , —N(R ) , —C(=O)OR , a a a a a a a a —C(=O)R , —C(=O)N(R ) , —N(R )C(=O)OR , —N(R )C(=O)N(R ) , —N(R )C(=O)R , a a a a a —N(R )S(=O) R (where t is 1 or 2), —N(R )S(=O) N(R ) (where t is 1 or 2), —S(=O) R t t 2 t (where t is 1 or 2), —S(=O) N(R ) (where t is 1 or 2), —OPO WY (where W and Y are t 2 3 independently hydrogen, methyl, ethyl, alkyl, lithium, sodium or potassium) or —OPO3Z (where Z is calcium, magnesium or iron), wherein each R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl.

The term “aromatic” or “aryl” refers to an aromatic radical with six to ten ring atoms (i.e., C6-C10 aromatic or C6-C10 aryl) which has at least one ring having a conjugated pi electron system which is carbocyclic (e.g., phenyl, fluorenyl, and naphthyl). Whenever it appears herein, a numerical range such as “6 to 10” refers to each integer in the given range; e.g., “6 to 10 ring atoms” means that the aryl group may consist of 6 ring atoms, 7 ring atoms, etc., up to and including 10 ring atoms. The term includes monocyclic or fused-ring polycyclic (i.e., rings which share adjacent pairs of ring atoms) groups. Unless stated otherwise specifically in the specification, an aryl moiety is optionally substituted by one or more substituents which are independently alkyl, heteroalkyl, alkenyl, allynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, cyano, nitro, oxo, thioxo, trimethylsilanyl, a a a a a a a —OR , —SR , —OC(=O)—R , —OC(=O)OR , —OC(=O)N(R ) , —N(R ) , —C(=O)R , a a a a a a a a —C(=O)OR , —C(=O)N(R ) , —N(R )C(=O)OR , —N(R )C(=O)N(R ) , —N(R )C(=O)R , a a a a a —N(R )S(=O) N(R ) (where t is 1 or 2), —N(R )S(=O) R (where t is 1 or 2), —S(=O) R t 2 t t (where t is 1 or 2), —S(=O) N(R ) (where t is 1 or 2), or —OPO WY (where W and Y are t 2 3 independently hydrogen, methyl, ethyl, alkyl, lithium, sodium or potassium) or —OPO Z (where Z is calcium, magnesium or iron), wherein each R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl.

The term “heteroaryl” or, alternatively, “heteroaromatic” refers to a 5- to 18- membered aromatic radical (i.e., C5-C18 heteroaryl) that includes one or more ring heteroatoms selected from nitrogen, oxygen and sulfur, and which may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system. Whenever it appears herein, a numerical range such as “5 to 18” refers to each integer in the given range; e.g., “5 to 18 ring atoms” means that the heteroaryl group may consist of 5 ring atoms, 6 ring atoms, etc., up to and including 18 ring atoms. An N-containing “heteroaromatic” or “heteroaryl” moiety refers to an aromatic group in which at least one of the skeletal atoms of the ring is a nitrogen atom. The polycyclic heteroaryl group may be fused or non-fused. The heteroatom(s) in the heteroaryl radical, e.g., nitrogen or sulfur, is optionally oxidized. One or more nitrogen atoms, if present, are optionally quaternized. The heteroaryl is attached to the rest of the molecule through any atom of the ring(s). Examples of heteroaryls include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzindolyl, 1,3-benzodioxolyl, benzooxazolyl, benzo[d]thiazolyl, benzothiadiazolyl, benzo[b][1,4]dioxepinyl, benzo[b][1,4]oxazinyl, 1,4-benzodioxanyl, benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl, benzoxazolyl, benzopyranyl, benzopyranonyl, benzofuranyl, benzofuranonyl, benzofurazanyl, benzothiazolyl, benzothienyl, benzothieno[3,2-d]pyrimidinyl, benzotriazolyl, benzo[4,6]imidazo[1,2-a]pyridinyl, carbazolyl, cinnolinyl, cyclopenta[d]pyrimidinyl, 6,7- dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidinyl, 5,6-dihydrobenzo[h]quinazolinyl, 5,6- dihydrobenzo[h]cinnolinyl, 6,7-dihydro-5H-benzo[6,7]cyclohepta[1,2-c]pyridazinyl, dibenzofuranyl, dibenzothiophenyl, furanyl, furazanyl, furanonyl, furo[3,2-c]pyridinyl, ,6,7,8,9,10-hexahydrocycloocta[d]pyrimidinyl, 5,6,7,8,9,10- hexahydrocycloocta[d]pyridazinyl, 5,6,7,8,9,10-hexahydrocycloocta[d]pyridinyl, isothiazolyl, imidazolyl, indazolyl, indolyl, indazolyl, isoindolyl, indolinyl, isoindolinyl, isoquinolyl, indolizinyl, isoxazolyl, 5,8-methano-5,6,7,8-tetrahydroquinazolinyl, naphthyridinyl, 1,6-naphthyridinonyl, oxadiazolyl, 2-oxoazepinyl, oxazolyl, oxiranyl, ,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazolinyl, 1-phenyl-1H-pyrrolyl, phenazinyl, phenothiazinyl, phenoxazinyl, phthalazinyl, pteridinyl, purinyl, pyranyl, pyrrolyl, pyrazolyl, pyrazolo[3,4-d]pyrimidinyl, pyridinyl, pyrido[3,2-d]pyrimidinyl, pyrido[3,4-d]pyrimidinyl, pyrazinyl, pyrimidinyl, pyridazinyl, pyrrolyl, quinazolinyl, quinoxalinyl, quinolinyl, isoquinolinyl, tetrahydroquinolinyl, 5,6,7,8-tetrahydroquinazolinyl, 5,6,7,8- tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidinyl, 6,7,8,9-tetrahydro-5H- cyclohepta[4,5]thieno[2,3-d]pyrimidinyl, 5,6,7,8-tetrahydropyrido[4,5-c]pyridazinyl, thiazolyl, thiadiazolyl, thiapyranyl, triazolyl, tetrazolyl, triazinyl, thieno[2,3-d]pyrimidinyl, thieno[3,2-d]pyrimidinyl, thieno[2,3-c]pridinyl, and thiophenyl (i.e. thienyl). Unless stated otherwise specifically in the specification, a heteroaryl moiety is optionally substituted by one or more substituents which are independently: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, cyano, nitro, oxo, thioxo, a a a a trimethylsilanyl, —SR , —OC(=O)—R , —OC(=O)OR , —N(R ) , a a a a a a —C(=O)OR , —OC(=O)N(R ) , —C(=O)R , —C(=O)N(R ) , —N(R )C(=O)OR , a a a a a a —N(R )C(=O)N(R ) , —N(R )C(=O)R , —N(R )S(=O) R (where t is 1 or 2), a a a a —N(R )S(=O) N(R ) (where t is 1 or 2), —S(=O) R (where t is 1 or 2), —S(=O) N(R ) t 2 t t 2 (where t is 1 or 2), —OPO WY (where W and Y are independently hydrogen, methyl, ethyl, alkyl, lithium, sodium or potassium) or —OPO Z (where Z is calcium, magnesium or iron), wherein each R is independently hydrogen, alkyl, heteroalkyl, cyclolalkyl, heterocycloalkyl, aryl or heteroaryl. Examples of monocylic heteroaryls include, but are not limited to, imidazolyl, pyridinyl, pyrrolyl, pyrazinyl, pyrimidinyl, thiazolyl, furanyl and thienyl.

The term “acyl” refers to a —(C=O)R radical, wherein R is alkyl, cycloalkyl, aryl, heteroaryl, heteroalkyl, or heterocycloalkyl, which are as described herein. The R group is joined to the carbonyl through a carbon-carbon single bond. In some embodiments, it is a C1-C10 acyl radical which refers to the total number of chain or ring atoms of the alkyl, cycloalkyl, aryl, heteroalkyl, heteroaryl or heterocycloalkyl portion of the acyl group plus the carbonyl carbon of acyl, i.e. ring or chain atoms plus carbonyl. If the R radical is heteroaryl or heterocycloalkyl, the hetero ring or chain atoms contribute to the total number of chain or ring atoms. Unless stated otherwise specifically in the specification, the R of an acyl group is optionally substituted by one or more substituents which independently are: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, cyano, trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl, —OR , —SR , —OC(=O)— a a a a a a R , —OC(=O)OR , —N(R ) , —C(=O)R , —C(=O)OR , —OC(=O)N(R ) , — a a a a a a a C(=O)N(R ) , —N(R )C(=O)OR , —N(R )C(=O)N(R ) , —N(R )C(=O)R , — a a a a a N(R )S(=O) R (where t is 1 or 2), —N(R )S(=O) N(R ) (where t is 1 or 2), —S(=O) R t t 2 t (where t is 1 or 2), —S(=O) N(R ) (where t is 1 or 2), or —P(=O)(OR ) , t 2 2 wherein each of R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl.

The term “halo”, “halide”, or alternatively, “halogen” means fluoro, chloro, bromo or iodo. The terms “haloalkyl”refers to alkyl structures that are substituted with one or more halo groups or combinations thereof. The terms “haloalkoxy” refers to alkoxy structures that are substituted with one or more halo groups or combinations thereof. The terms “fluoroalkyl” and “fluoroalkoxy” refer to haloalkyl and haloalkoxy groups, respectively, in which the halo is fluoro. Examples of fluoroalkyl include, but are not limited to, —CH F, —CHF , —CF , —CF CH —CH CF , and —CF CF . 2 3 2 3, 2 3 2 3 The term “cyano” refers to a —CN radical.

The term “alkoxy” refers to an — O—alkyl radical, wherein alkyl is as described herein and contains 1 to 10 carbons (i.e., C1-C10 alkoxy). Whenever it appears herein, a numerical range such as “1 to 10” refers to each integer in the given range; e.g., “1 to 10 carbon atoms” means that the alkyl group may consist of 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc., up to and including 10 carbon atoms. In some embodiments, it is a C1-C4 alkoxy group. Unless stated otherwise specifically in the specification, an alkoxy moiety may be substituted by one or more of the substituents described as suitable substituents for an alkyl radical.

The term “sp hybridized carbon” refers to a carbon atom that is bonded to four other atoms. sp hybridization results from the combination of the s orbital and all three p orbitals in the second energy level of carbon. It results in four equivalent orbitals and the geometric arrangement of those four orbitals is tetrahedral.

The term “sulfonyl” refers to a —S(=O)2—R radical, wherein R is selected from the group consisting of alkyl, cycloalkyl, aryl, heteroalkyl, heteroaryl (bonded through a ring carbon) and heterocycloalkyl (bonded through a ring carbon). Unless stated otherwise specifically in the specification, the R group may be substituted by one or more of the substituents described as suitable substituents for an alkyl, an aryl or a heteroaryl radical. a b a The term “sulfoximinyl” refers to a —S(=O)(=NR ) —R radical, wherein R is selected from the group consisting of hydrogen, alkyl, cycloalkyl, aryl, cyano, carbamoyl, acyl, heteroaryl (bonded through a ring carbon) and heterocycloalkyl (bonded through a ring carbon) and R is independently selected from the group consisting of alkyl, cycloalkyl, aryl, heteroalkyl, heteroaryl (bonded through a ring carbon) and heterocycloalkyl (bonded through a ring carbon). Unless stated otherwise specifically in the specification, the R and R group may be substituted by one or more of the substituents described as suitable substituents for an alkyl, an aryl or a heteroaryl radical.

The term “sulfonamide” refers to a —S(=O) —N(R ) radical, wherein each R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl or heterocycloalkyl, and at least one R is hydrogen.

The term “cycloalkyl” refers to a monocyclic or polycyclic non-aromatic radical that contains carbon and hydrogen, and may be saturated, or partially unsaturated.

Cycloalkyl groups include groups having from 3 to 10 ring atoms (i.e., C3-C10 cycloalkyl).

Whenever it appears herein, a numerical range such as “3 to 10” refers to each integer in the given range; e.g., “3 to 10 carbon atoms” means that the cycloalkyl group may consist of 3 carbon ring atoms, 4 carbon ring atoms, 5 carbon ring atoms, etc., up to and including 10 carbon ring atoms. In some embodiments, it is a C3-C5 cycloalkyl radical. Illustrative examples of cycloalkyl groups include, but are not limited to the following moieties: cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloseptyl, cyclooctyl, cyclononyl, cyclodecyl, and the like. Unless stated otherwise specifically in the specification, a cycloalkyl group is optionally substituted by one or more substituents which independently are: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, a a a a cyano, nitro, oxo, thioxo, trimethylsilanyl, —OR , —SR , —OC(=O)—R , —OC(=O)OR , a a a a a a a —OC(=O)N(R ) , —N(R ) , —C(=O)R , —C(=O)OR , —C(=O)N(R ) , —N(R )C(=O)OR , 2 2 2 a a a a a a —N(R )C(=O)N(R ) , —N(R )C(=O)R , —N(R )S(=O) R (where t is 1 or 2), a a a —N(R )S(=O)tN(R )2 (where t is 1 or 2), —S(=O)tR (where t is 1 or 2), —S(=O) N(R ) (where t is 1 or 2), —OPO WY (where W and Y are independently t 2 3 hydrogen, methyl, ethyl, alkyl, lithium, sodium or potassium) or —OPO3Z (where Z is calcium, magnesium or iron), wherein each R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl.

The term “heterocyclyl” or “heterocycloalkyl” refers to a stable and not fully aromatic 3- to 18-membered ring (i.e., C3-C18 heterocycloalkyl) radical that comprises two to twelve ring carbon atoms and from one to six ring heteroatoms selected from nitrogen, oxygen and sulfur. Whenever it appears herein, a numerical range such as “3 to 18” refers to each integer in the given range; e.g., “3 to 18 ring atoms” means that the heterocycloalkyl group may consist of 3 ring atoms, 4 ring atoms, etc., up to and including 18 ring atoms. In some embodiments, it is a C5-C10 heterocycloalkyl. In some embodiments, it is a C4-C10 heterocycloalkyl. In some embodiments, it is a C3-C10 heterocycloalkyl. Unless stated otherwise specifically in the specification, the heterocycloalkyl radical may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems. The heteroatoms in the heterocycloalkyl radical may be optionally oxidized. One or more nitrogen atoms, if present, may optionally be quaternized. The heterocycloalkyl radical may be partially or fully saturated. The heterocycloalkyl may be attached to the rest of the molecule through any atom of the ring(s). Examples of such heterocycloalkyl radicals include, but are not limited to, 6,7-dihydro-5H-cyclopenta[b]pyridine, dioxolanyl, thienyl[1,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2-oxopiperazinyl, 2- oxopiperidinyl, 2-oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4-piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl, 1-oxo-thiomorpholinyl, and 1,1-dioxo- thiomorpholinyl. Unless stated otherwise specifically in the specification, a heterocycloalkyl moiety is optionally substituted by one or more substituents which independently are: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, a a a a cyano, nitro, oxo, thioxo, trimethylsilanyl, —OR , —SR , —OC(=O)—R , —OC(=O)OR , a a a a a a a —OC(=O)N(R ) , —N(R ) , —C(=O)R , —C(=O)OR , —C(=O)N(R ) , —N(R )C(=O)OR , 2 2 2 a a a a a a —N(R )C(=O)N(R ) , —N(R )C(=O)R , —N(R )S(=O) R (where t is 1 or 2), a a a a —N(R )S(=O) N(R ) (where t is 1 or 2), —S(=O) R (where t is 1 or 2), —S(=O) N(R ) t 2 t t 2 (where t is 1 or 2), —OPO WY (where W and Y are independently hydrogen, methyl, ethyl, alkyl, lithium, sodium or potassium) or —OPO3Z (where Z is calcium, magnesium or iron), wherein each R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl.

The terms “heteroalkyl”, “heteroalkenyl” and “heteroalkynyl” include optionally substituted alkyl, alkenyl and alkynyl radicals, which respectively have one or more skeletal chain atoms selected from an atom other than carbon, e.g., oxygen, nitrogen, sulfur, phosphorus or combinations thereof. A numerical range, which refers to the chain length in total, may be given. For example, C3-C4 heteroalkyl has a chain length of 3-4 atoms. For example, a —CH OCH CH radical is referred to as a “C4 heteroalkyl”, which 2 2 3 includes the heteroatom in the atom chain length description. Connection to the rest of the molecule is through a carbon in the heteroalkyl chain. A heteroalkyl may be a substituted alkyl. The same definition applies to heteroalkenyl or heteroalkynyl. Unless otherwise stated in the specification, a heteroalkyl group may be substituted with one or more substituents which independently are: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, cyano, nitro, oxo, thioxo, trimethylsilanyl, —OR , —SR , a a a a a a —OC(=O)—R , —OC(=O)OR , —OC(=O)N(R ) , —N(R ) , —C(=O)R , —C(=O)OR , a a a a a a a —C(=O)N(R ) , —N(R )C(=O)OR , —N(R )C(=O)N(R ) , —N(R )C(=O)R , a a a a —N(R )S(=O) R (where t is 1 or 2), —N(R )S(=O) N(R ) (where t is 1 or 2), —S(=O) R t a t 2 t (where t is 1 or 2), —S(=O) N(R ) (where t is 1 or 2), —OPO WY (where W and Y are t 2 3 independently hydrogen, methyl, ethyl, alkyl, lithium, sodium or potassium) or —OPO Z (where Z is calcium, magnesium or iron), wherein each R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl.

The term “amino” or “amine” refers to a —NH radical group, The term “acyloxy” refers to a R(C=O)O— radical wherein R is alkyl, cycloalkyl, aryl, heteroalkyl, heteroaryl or heterocycloalkyl, which are as described herein. In some embodiments, it is a C2-C4 acyloxy radical, wherein the C2-C4 refers to the total number, i.e., 1-3 of the chain or ring atoms of the alkyl, cycloalkyl, aryl, heteroalkyl, heteroaryl or heterocycloalkyl portion of the acyloxy group plus the carbonyl carbon of acyl, i.e., the ring or chain atoms plus carbonyl. If the R radical is heteroaryl or heterocycloalkyl, the hetero ring or chain atoms contribute to the total number of chain or ring atoms. Unless stated otherwise specifically in the specification, the R of an acyloxy group is optionally substituted by one or more of the following substituents: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, cyano, nitro, oxo, thioxo, a a a a a trimethylsilanyl, —OR , —SR , —OC(=O)—R , —OC(=O)OR , —OC(=O)N(R ) , — a a a a a a N(R )2, —C(=O)R , —C(=O)OR , —C(=O)N(R )2, —N(R )C(=O)OR , — a a a a a a N(R )C(=O)N(R ) , —N(R )C(=O)R , —N(R )S(=O) R (where t is 1 or 2), — a a a a N(R )S(=O)tN(R )2 (where t is 1 or 2), —S(=O)tR (where t is 1 or 2), —S(=O)tN(R )2 (where t is 1 or 2), —OPO WY (where W and Y are independently hydrogen, methyl, ethyl, alkyl, lithium, sodium or potassium) or —OPO3Z (where Z is calcium, magnesium or iron), wherein each of R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl.

The term “alkenyl” refers to a straight or branched hydrocarbon chain radical group comprising carbon and hydrogen atoms, containing at least one double bond, and having from two to ten carbon atoms (i.e., C2-C10 alkenyl). Whenever it appears herein, a numerical range such as “2 to 10” refers to each integer in the given range; e.g., “2 to 10 carbon atoms” means that the alkenyl group may contain 2 carbon atoms, 3 carbon atoms, etc., up to and including 10 carbon atoms. In certain embodiments, an alkenyl comprises two to eight carbon atoms (i.e., C2-C8 alkenyl). In other embodiments, an alkenyl comprises two to five carbon atoms (i.e., C2-C5 alkenyl). The alkenyl is attached to the rest of the molecule by a single bond, for example, ethenyl (i.e., vinyl), propenyl, butenyl, pentenyl, penta-1,4-dienyl, and the like. Unless stated otherwise specifically in the specification, an alkenyl group is optionally substituted by one or more of the following substituents: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, a a a a cyano, nitro, oxo, thioxo, trimethylsilanyl, —OR , —SR , —OC(=O)—R , —OC(=O)OR , a a a a a a a —OC(=O)N(R ) , —N(R ) , —C(=O)R , —C(=O)OR , —C(=O)N(R ) , —N(R )C(=O)R , 2 2 2 a a a a a a —N(R )C(=O)OR , —N(R )C(=O)N(R ) , —N(R )S(=O) R (where t is 1 or 2), a a a a —N(R )S(=O) N(R ) (where t is 1 or 2), —S(=O) R (where t is 1 or 2), —S(=O) N(R ) t 2 t t 2 (where t is 1 or 2), —OPO WY (where W and Y are independently hydrogen, methyl, ethyl, alkyl, lithium, sodium or potassium) or —OPO Z (where Z is calcium, magnesium or iron), wherein each of R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl.

The term “alkynyl” refers to a straight or branched hydrocarbon chain radical group comprising carbon and hydrogen atoms, containing at least one triple bond, and having from two to ten carbon atoms (i.e., C2-C10 alkynyl). In some embodiments, an alkynyl group may contain one or more double bonds. Whenever it appears herein, a numerical range such as “2 to 10” refers to each integer in the given range; e.g., “2 to 10 carbon atoms” means that the alkynyl group may contain 2 carbon atoms, 3 carbon atoms, etc., up to and including 10 carbon atoms. In certain embodiments, an alkynyl comprises two to eight carbon atoms (i.e., C2-C8 alkynyl). In other embodiments, an alkynyl has two to five carbon atoms (i.e., C2-C5 alkynyl). The alkynyl is attached to the rest of the molecule by a single bond, for example, ethynyl, propynyl, butynyl, pentynyl, hexynyl, and the like. Unless stated otherwise specifically in the specification, an alkynyl group is optionally substituted by one or more of the following substituents: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, cyano, nitro, oxo, thioxo, trimethylsilanyl, —OR , —SR , a a a a a a —OC(=O)—R , —OC(=O)OR , —OC(=O)N(R ) , —N(R ) , —C(=O)R , —C(=O)OR , a a a a a a a —C(=O)N(R ) , —N(R )C(=O)OR , —N(R )C(=O)R , —N(R )C(=O)N(R ) , a a a a a —N(R )S(=O) R (where t is 1 or 2), —N(R )S(=O) N(R ) (where t is 1 or 2), —S(=O) R t t 2 t (where t is 1 or 2), —S(=O) N(R ) (where t is 1 or 2), —OPO WY (where W and Y are t 2 3 independently hydrogen, methyl, ethyl, alkyl, lithium, sodium or potassium) or —OPO Z (where Z is calcium, magnesium or iron), wherein each R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl.

The term “alkylamino” refers to a chemical moiety with formula —N(R ) , wherein each R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, or heterocycloalkyl, and at least one R is not hydrogen. Two R s may optionally form a 3-8 membered ring.

The term “amide” or “amido” refers to a chemical moiety with formula a a a a —C(=O)N(R ) or —NR C(=O)R , wherein each of R is independently selected from the group consisting of hydrogen, alkyl, cycloalkyl, aryl, heteroaryl (bonded through a ring carbon) and heterocycloalkyl. Two R s, together with the atoms they are attached to, optionally form a 5-10 membered ring. In some embodiments, it is a C1-C4 amido or amide radical, which includes the amide carbonyl in the total number of carbons in the radical.

Unless stated otherwise specifically in the specification, an amido group is optionally substituted independently by one or more of the substituents as described herein for alkyl, cycloalkyl, aryl, heteroaryl, or heterocycloalkyl. An amino acid or a peptide molecule may be attached to a compound having an amine or a carboxylic acid moiety, thereby forming a prodrug. The procedures and specific groups to make such amides are known to those of skilled in the art and can readily be found in reference sources such as Greene and Wuts, Protective Groups in Organic Synthesis, 3rd Ed., John Wiley & Sons, New York, N.Y., 1999.

“Carboxaldehyde” refers to a —(C=O)H radical.

“Carboxylic acid” refers to a —(C=O)OH radical.

“Ester” refers to a chemical radical of formula —C(=O)OR, where R is selected from the group consisting of alkyl, cycloalkyl, aryl, heteroaryl (bonded through a ring carbon) and heteroalkyl (bonded through a ring carbon). A hydroxy or carboxylic acid moiety on the compounds described herein may be esterified. The procedures and specific groups to make such esters are known to those skilled in the art and can readily be found in reference sources such as Greene and Wuts, Protective Groups in Organic Synthesis, 3rd Ed., John Wiley & Sons, New York, N.Y., 1999. Unless stated otherwise specifically in the specification, an ester group is optionally substituted by one or more substituents which independently are: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, halo, cyano, nitro, oxo, thioxo, trimethylsilanyl, —OR , —SR , a a a a a a —OC(=O)—R , —OC(=O)OR , —OC(=O)N(R ) , —N(R ) , —C(=O)R , —C(=O)OR , a a a a a a a —C(=O)N(R ) , —N(R )C(=O)OR , —N(R )C(=O)N(R ) , —N(R )C(=O)R , a a a a a —N(R )S(=O) R (where t is 1 or 2), —N(R )S(=O) N(R ) (where t is 1 or 2), —S(=O) OR t t 2 t (where t is 1 or 2), —S(=O) N(R ) (where t is 1 or 2), —OPO WY (where W and Y are t 2 3 independently hydrogen, methyl, ethyl, alkyl, lithium, sodium or potassium) or —OPO Z (where Z is calcium, magnesium or iron), wherein each of R is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl.

“Imino” refers to a =N—R radical, wherein R is hydrogen, alkyl, heteroalkyl, cycloalkyl, cyano, aryl, heterocycloalkyl or heteroaryl.

“Isocyanato” refers to a —NCO radical.

“Isothiocyanato” refers to a —NCS radical.

“Mercaptyl” refers to an (alkyl)S— or (H)S— radical.

“Moiety” refers to a specific segment or functional group of a molecule.

Chemical moieties are often recognized chemical entities embedded in or appended to a molecule.

“Hydroxy” refers to a —OH radical.

“Oxa” refers to a —O— radical.

“Oxo” refers to a =O radical.

“Nitro” refers to a —NO radical.

“Oxime” refers to a —C(=N-OH)—R radical, where R is hydrogen or alkyl.

“Sulfinyl” refers to a —S(=O)—R radical, where R is selected from the group consisting of alkyl, cycloalkyl, aryl, heteroalkyl, heteroaryl (bonded through a ring carbon) and heterocyclyl (bonded through a ring carbon). In some embodiments, R is fluoroalkyl.

“Sulfoxyl” refers to a —S(=O) OH radical.

“Sulfonate” refers to a —S(=O) —OR radical, where R is selected from the group consisting of alkyl, cycloalkyl, aryl, heteroalkyl, heteroaryl (bonded through a ring carbon) and heteroalkyl (bonded through a ring carbon). The R group is optionally substituted by one or more of the subsituents described for alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl respectively.

“Thiocyanato” refers to a —CNS radical.

“Thioxo” refers to a =S radical.

“Substituted” means that the referenced group may be substituted with one or more additional group(s) individually and independently selected from acyl, alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, alkoxy, mercapto, alkylthio, arylthio, cyano, halo, carbonyl, ester, thiocarbonyl, isocyanato, thiocyanato, isothiocyanato, nitro, perhaloalkyl, perfluoroalkyl, phosphate, silyl, sulfinyl, sulfonyl, sulfonamide, sulfoximinyl, alkylamino, and amino, and the protected derivatives thereof. The substituents themselves may be substituted, for example, a cycloalkyl substituent may have a halide substituted at one or more ring carbons, and the like. The protecting groups that may form the protective derivatives of the above substituents are known to those of skill in the art and may be found in references such as Greene and Wuts cited herein.

The term “optional” or “optionally” means that the subsequently described event or circumstance may or may not occur, and includes instances where the event or circumstance occurs and instances in which it does not. For example, “alkyl optionally substituted with” encompasses both “alkyl” and “alkyl” substituted with groups as defined herein. It will be understood by those skilled in the art, with respect to any group containing one or more substituents, that such groups are not intended to introduce any substitution or substitution patterns which would be deemed unacceptable by one of ordinary skill in the art. [065a] The term “comprising” as used in this specification and claims means “consisting at least in part of”. When interpreting statements in this specification and claims which include the term “comprising”, other features besides the features prefaced by this term in each statement can also be present. Related terms such as “comprise” and “comprises” are to be interpreted in similar manner.

The methods and formulations described herein include the use of N-oxides, crystalline forms (also known as polymorphs), or pharmaceutically acceptable salts of compounds having the structure of formulae described herein, as well as active metabolites of these compounds having the same type of activity. In addition, the compounds described herein can exist in unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like. The solvated forms of the compounds presented herein are also considered to be disclosed herein.

The compounds described herein may exhibit their natural isotopic abundance, or one or more of the atoms may be artificially enriched in a particular isotope having the same atomic number, but an atomic mass or mass number different from the atomic mass or mass number predominantly found in nature. The present invention is meant to include all suitable isotopic variations of the compounds described herein. For example, hydrogen has 1 2 3 three naturally occurring isotopes, denoted H (protium), H (deuterium), and H (tritium).

Protium is the most abundant isotope in nature. Enriching for deuterium may afford certain therapeutic advantages, such as increased in vivo half-life and/or exposure, or may provide a compound useful for investigating in vivo routes of drug elimination and metabolism.

Isotopically-enriched compounds may be prepared by conventional techniques well known to those skilled in the art or by processes analogous to those described in the Schemes and Examples herein using appropriate isotopically-enriched reagents and/or intermediates. See Pleiss and Voger, Synthesis and Applications of Isotopically Labeled Compounds, Vol. 7, Wiley, ISBN-10: 0471495018, published on March 14, 2001.

Unless otherwise specified, chemical entities described herein may include, but are not limited to, when possible, their optical isomers, such as enantiomers and diastereomers, mixtures of enantiomers, including racemates, mixtures of diastereomers, and other mixtures thereof, to the extent they can be made by one of ordinary skill in the art by routine experimentation. In those situations, the single enantiomers or diastereomers, i.e., optically active forms, can be obtained by asymmetric synthesis or by resolution of the racemates or mixtures of diastereomers. Resolution of the racemates or mixtures of diastereomers, if needed, can be accomplished, for example, by conventional methods such as crystallization in the presence of a resolving agent, or chromatography, using, for example, a chiral high-pressure liquid chromatography (HPLC) column. In addition, chemical entities having carbon-carbon double bonds or carbon-nitrogen double bonds may exist in Z- or E- form (or cis- or trans- form). Furthermore, some chemical entities may exist in various tautomeric forms. Unless otherwise specified, chemical entities described herein are intended to include all Z-, E- and tautomeric forms as well.

The term "pharmaceutically acceptable" means that a chemical entity, such as a compound, a carrier, an additive or a salt, is acceptable for being administrated to a subject.

The term "pharmaceutically acceptable salts" refers to salts prepared from pharmaceutically acceptable bases or acids including inorganic or organic bases and inorganic or organic acids. Salts derived from inorganic bases may be selected, for example, from aluminum, ammonium, calcium, copper, ferric, ferrous, lithium, magnesium, manganic, manganous, potassium, sodium, and zinc salts. Further, for example, the pharmaceutically acceptable salts derived from inorganic bases may be selected from ammonium, calcium, magnesium, potassium, and sodium salts. Salts derived from pharmaceutically acceptable organic bases may be selected, for example, from salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines, and basic ion exchange resins, such as arginine, betaine, caffeine, choline, N,N'- dibenzylethylene-diamine, diethylamine, 2-diethylaminoethanol, 2-dimethylaminoethanol, ethanolamine, ethylenediamine, N-ethyl-morpholine, N-ethylpiperidine, glucamine, glucosamine, histidine, hydrabamine, isopropylamine, lysine, methylglucamine, morpholine, piperazine, piperidine, polyamine resins, procaine, purines, theobromine, triethylamine, trimethylamine, tripropylamine, and tromethamine.

When chemical entities disclosed herein are basic, salts may be prepared using at least one pharmaceutically acceptable acid, selected from inorganic and organic acids.

Such acid may be selected, for example, from acetic, benzenesulfonic, benzoic, camphorsulfonic, citric, ethanesulfonic, fumaric, gluconic, glutamic, hydrobromic, hydrochloric, isethionic, lactic, maleic, malic, mandelic, methanesulfonic, mucic, nitric, pamoic, pantothenic, phosphoric, succinic, sulfuric, tartaric, trifluoroacetic acid, and p- toluenesulfonic acids. In some embodiments, such acid may be selected, for example, from citric, hydrobromic, hydrochloric, maleic, phosphoric, sulfuric, fumaric, and tartaric acids.

The term "pharmaceutically acceptable carrier" as used herein means a diluent, excipient, encapsulating material or formulation auxiliary, which may be non-toxic, and inert, which may not have undesirable effect on a subject, preferably a mammal, more preferably a human, or which may be suitable for delivering an active agent to the target site without affecting the activity of the agent.

The term "enantiomeric excess," as used herein, is the percent excess of one enantiomer compared to that of the other enantiomer in a mixture, and can be calculated using the following equation: enantiomeric excess = ((R-S) / (R+S)) x 100 = %(R*) - %(S*), wherein R and S are the number of moles of each enantiomer in the mixture, and R* and S* are the respective mole fractions of the enantiomers in the mixture. For example, for a mixture with 87% R enantiomer and 13% S enantiomer, the enantiomeric excess is 74%.

The term “effective amount” or “therapeutically effective amount” refers to an amount of a compound or pharmaceutical composition described herein that is sufficient to effect the intended application including, but not limited to, disease treatment, as illustrated below. The therapeutically effective amount can vary depending upon the intended application (in vitro or in vivo), or the subject and disease condition being treated, e.g., the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art. The specific dose will vary depending on, for example, the particular compounds chosen, the dosing regimen to be followed, whether it is administered in combination with other agents, timing of administration, the tissue to which it is administered, and the physical delivery system in which it is carried.

The term “about” refers to ±10% of a stated number or value.

The following abbreviations and terms have the indicated meanings throughout: DAST = Diethylaminosulfur trifluoride DCM = Dichloromethane MTBE = Methyl t-butyl ether HATU = O-(7-azabenzotriazolyl)-N,N,N ′,N ′-tetramethyluronium hexafluorophosphate NBS = N-Bromosuccinimide NMP = N-Methylpyrrolidone e.e. or ee = Enantiomeric excess PPTS = Pyridinium p-toluenesulfonate DMAP = 4-Dimethylaminopyridine DMF = N,N-Dimethylformamide Compounds When “ ” is drawn across a bond, it denotes where a bond disconnection or attachment occurs. For example, in the chemical structure shown below, R1 group is attached to the para position of a fluorophenyl ring through a single bond. When R1 is phenyl, it can also be drawn as “ ”.

The waved line “ ” means a bond with undefined stereochemistry. For example, represents a mixture of and .

When a bond is drawn across a ring, it means substitution at a non-specific ring atom or position. For example, in the structure shown below, R may be attached to any one of the –CH – in the five-membered ring.

Described herein is a compound having the structure of Formula I or a pharmaceutically acceptable salt thereof, wherein: R is aryl or heteroaryl; R is nitro, carboxaldehyde, carboxylic acid, ester, amido, cyano, halo, sulfonyl or alkyl; R is hydrogen, halo, cyano, alkyl, heteroalkyl, alkenyl, alkynyl, alkylamino, carboxaldehyde, carboxylic acid, oxime, ester, amido or acyl, or R /R and atoms they are attached to form a 5- or 6-membered carbocycle with at least one sp hybridized carbon; R is nitro, halo, cyano, alkyl, sulfinyl, sulfonamide, sulfonyl or sulfoximinyl; and R5 is hydrogen, halo or alkyl.

In some embodiments, R is phenyl or monocyclic heteroaryl. In some further embodiments, R1 is phenyl or pyridyl, optionally substituted with one or more substituents selected from the group consisting of halo, alkyl, alkoxy, and cyano. In a further embodiment, the substituent(s) is selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R1 is wherein the aryl ring may optionally be substituted with one or more substituents selected from the group consisting of cyano, halo, alkyl and alkoxy. In a further embodiment, the substituent(s) is selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R is wherein X is N or CR , R is cyano, halo, alkyl or alkoxy, and R is hydrogen, cyano, 7 6 7 halo, alkyl or alkoxy. In a further embodiment, R is cyano, halo, C1-C4 alkyl or C1-C4 alkoxy, and R is hydrogen, cyano, halo, C1-C4 alkyl or C1-C4 alkoxy.

In some embodiments, R is pyridyl N-oxide. In a further embodiment, the pyridyl N-oxide is substituted with one or more substituents selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R is bicyclic heteroaryl. In a further embodiment, the bicyclic heteroaryl is substituted with one or more substituents selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R is selected from the group consisting of: , and the rings specified for R may optionally be substituted by one or more substituents described for aryl and heteroaryl. In a further embodiment, the substituent(s) is selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R is cyano, halo or alkyl. In some embodiments, R is halo or alkyl. In some embodiments, R is fluoro, chloro, bromo or iodo. In some embodiments, R is fluoroalkyl. In some further embodiments, R is —CH F, —CHF or 2 2 2 2, —CF .

In some embodiments, R is hydrogen, halo, cyano, alkyl, heteroalkyl or acyl; or R /R and atoms they are attached to may optionally form a 5- or 6-membered carbocycle with at least one sp hybridized carbon. In a further embodiment, R is halo, cyano or alkyl.

In yet a further embodiment, R is —(CH ) OH, wherein n is 1, 2, or 3. In still a further 3 2 n embodiment, n is 1.

In some embodiments, R /R and atoms they are attached to form a 5- or 6- membered carbocycle with at least one sp carbon. Representative compounds with the carbocycle include, but are not limited to, the following: wherein the carbocycle formed by linking R and R may be optionally substituted with fluoro, chloro, hydroxy, alkyl, or heteroalkyl. In a further embodiment, the substituent(s) is selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R is hydrogen, R is —S(=O) R or 3 4 2 a —S(=O)(=NRb)Rc, wherein Ra is fluoroalkyl, Rb is hydrogen, cyano or alkyl and Rc is alkyl.

In a further embodiment, R is selected from the group consisting of wherein: X is N or CR , R is cyano, halo, alkyl or alkoxy, and R is hydrogen, cyano, halo, 7 6 7 alkyl or alkoxy; and may optionally be substituted with one or more substituents selected from the group consisting of cyano, halo, alkyl and alkoxy. In a further embodiment, the alkyl is C1-C4 alkyl. In another further embodiment, the alkoxy is C1-C4 alkoxy.

In some embodiments, R is halo, cyano, fluoroalkyl, sulfinyl, sulfonamide, sulfonyl or sulfoximinyl. In some embodiments, R is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl or sulfoximinyl. In some embodiments, R is fluoroalkyl, sulfonamide, sulfonyl or sulfoximinyl.

In some embodiments, R is —S(=O) R , wherein R is alkyl or cycloalkyl. In 4 2 a a a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines.

Suitable examples of fluorine-substituted C1-C4 alkyl include, but are not limited to, — CH F, —CHF , —CF , —CH CF , —CH CHF , —CH CH F, —CHFCH , and —CF CH . In still a 2 3 2 3 2 2 2 2 3 2 3 further embodiment, R is methyl, optionally substituted with one or more fluorines.

In some embodiments, R is —S(=O)(=NR )R , wherein R is alkyl or 4 b a a cycloalkyl and R is hydrogen, cyano, or alkyl. In a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines. Suitable examples of fluorine-substituted C1-C4 alkyl include, but are not limited to, —CH F, —CHF , —CF , —CH CF , 2 2 3 2 3 —CH CHF , —CH CH F, —CHFCH , and —CF CH . 2 2 2 2 3 2 3 In some embodiments, R is —S(=O) —N(R ) , wherein each R is 4 2 a 2 a independently hydrogen, alkyl, heteroalkyl, cycloalkyl or heterocycloalkyl, and at least one R is hydrogen. In a further embodiment, both R s are hydrogen. In another further embodiment, one R is hydrogen and the other R is C1-C4 alkyl.

In some embodiments, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , 3 3 2 3 2 2 2 2 2 3 —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 2 2 3 3 2 —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, 2 3 3 2 —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF .

In some embodiments, R is hydrogen. In some other embodiments, R is C1- C4 alkyl. In a further embodiment, R is methyl.

In some embodiments, each of R and R is independently alkyl and R is 2 3 4 cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl or sulfoximinyl.

In some embodiments, R is —CH OH. In a further embodiment, R is cyano, 3 2 4 fluoroalkyl, sulfonamide, sulfinyl, sulfonyl or sulfoximinyl and R is hydrogen. In still a further embodiment, R is cyano, halo, or alkyl.

In some embodiments, R is phenyl or monocyclic heteroaryl; R is nitro, halo, cyano or alkyl; R is halo, cyano or alkyl; R is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl or sulfoximinyl. In a further embodiment, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , 3 3 2 3 2 2 2 2 2 3 —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 2 2 3 3 2 —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, 2 3 3 2 —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF . In still a further embodiment, R is 2 3 5 hydrogen.

In some embodiments, R is bicyclic heteroaryl; R is nitro, halo, cyano or alkyl; R is halo, cyano or alkyl; R is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl or sulfoximinyl; and R is hydrogen.

In some embodiments, R is phenyl, monocyclic heteroaryl, or bicyclic heteroaryl; R is halo, cyano or alkyl; R is halo, cyano or alkyl; R is cyano, fluoroalkyl, 2 3 4 sulfonamide, sulfinyl, sulfonyl or sulfoximinyl; R is hydrogen; and R is —CH OH. 3 2 In some embodiments, R and R and the atoms they are attached to form a 5- or 6-membered carbocycle with at least one sp carbon; R is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl or sulfoximinyl; and R is hydrogen. In a further embodiment, R is phenyl or monocyclic heteroaryl. In another further embodiment, R is bicyclic heteroaryl.

Described herein is a compound having the structure of Formula IIa R O R or a pharmaceutically acceptable salt thereof, wherein: R is nitro, carboxaldehyde, carboxylic acid, ester, amido, cyano, halo, sulfonyl or alkyl; R is hydrogen, halo, cyano, oxime, alkyl, heteroalkyl, alkenyl, alkynyl, alkylamino or acyl, or R /R and atoms they are attached to form a 5- or 6-membered carbocycle with at least one sp hybridized carbon; R is nitro, halo, cyano, alkyl, sulfinyl, sulfonamide, sulfonyl, or sulfoximinyl; R is hydrogen, halo or alkyl.

X is N or CR ; R is cyano, halo, alkyl, or alkoxy; and R is hydrogen, cyano, halo, alkyl, or alkoxy.

In some embodiments, R is cyano, halo, or alkyl. In some embodiments, R is halo or alkyl. In some embodiments, R is fluoro, chloro, bromo, or iodo. In some embodiments, R is fluoroalkyl. In some further embodiments, R is —CH F, —CHF , or 2 2 2 2 —CF .

In some embodiments, R is hydrogen, halo, cyano, alkyl, heteroalkyl, or acyl; or R /R and atoms they are attached to may optionally form a 5- or 6-membered carbocycle with at least one sp hybridized carbon.

In some embodiments, R is halo, cyano, or alkyl. In a further embodiment, R is –(CH ) OH, wherein n is 1, 2 or 3 .

In some embodiments, R /R and atoms they are attached to form a 5- or 6- membered carbocycle with at least one sp carbon. Representative compounds with the carbocycle include, but are not limited to, the following: 6 R O 4 X R X R 4 6 R O 4 X R wherein the carbocycle formed by linking R and R may be optionally substituted with fluoro, chloro, hydroxy, alkyl, or heteroalkyl. In a further embodiment, the substituent(s) is selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R is hydrogen, R is —S(=O) R or 3 4 2 a —S(=O)(=NR )R , wherein R is fluoroalkyl and R is hydrogen, cyano, or alkyl. b a a b In some embodiments, R is halo, cyano, fluoroalkyl, sulfinyl, sulfonamide, sulfonyl or sulfoximinyl. In some embodiments, R is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl, or sulfoximinyl. In some embodiments, R is fluoroalkyl, sulfonamide, sulfonyl, or sulfoximinyl.

In some embodiments, R is —S(=O) R , wherein R is alkyl or cycloalkyl. In 4 2 a a a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines.

Suitable examples of fluorine-substituted C1-C4 alkyl include, but are not limited to, — CH F, —CHF , —CF , —CH CF , —CH CHF , —CH CH F, —CHFCH , and —CF CH . In still a 2 3 2 3 2 2 2 2 3 2 3 further embodiment, R is methyl, optionally substituted with one or more fluorines.

In some embodiments, R is —S(=O)(=NR )R , wherein R is alkyl or 4 b a a cycloalkyl and R is hydrogen, cyano, or alkyl. In a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines. Suitable examples of fluorine-substituted C1-C4 alkyl include, but are not limited to, –CH F, –CHF , –CF , –CH CF , –CH CHF , 2 2 3 2 3 2 2 –CH CH F, –CHFCH , and –CF CH . 2 2 3 2 3 In some embodiments, R is —S(=O) —N(R ) , wherein each R is 4 2 a 2 a independently hydrogen, alkyl, heteroalkyl, cycloalkyl, or heterocycloalkyl, and at least one R is hydrogen. In a further embodiment, both R s are hydrogen. In another further embodiment, one R is hydrogen and the other R is C1-C4 alkyl.

In some embodiments, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , 3 3 2 3 2 2 2 2 2 3 —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 2 2 3 3 2 —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, 2 3 3 2 —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF .

In some embodiments, R is hydrogen. In some other embodiments, R is C1- C4 alkyl. In a further embodiment, R is methyl.

In some embodiments, R is cyano, halo, C1-C4 alkyl, or C1-C4 alkoxy.

In some embodiments, R is hydrogen, cyano, halo, C1-C4 alkyl, or C1-C4 alkoxy.

In some embodiments, R /R and atoms they are attached to form a 5- or 6- membered carbocycle with at least one sp carbon and R4 is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl, or sulfoximinyl.

In some embodiments, R3 is —CH2OH and R4 is cyano, fluoroalkyl, sulfonamide, sulfonyl, or sulfoximinyl. In a further embodiment, R is halo, cyano, or alkyl.

In still a further embodiment, R5 is hydrogen.

In some embodiments, R is halo, cyano or alkyl; R is —CH OH; R is 2 3 2 4 cyano, fluoroalkyl, sulfonamide, sulfonyl, or sulfoximinyl; R is hydrogen; X is N or CR ; R 7 7 is halo, cyano or C1-C4 alkyl; and R is halo, cyano or C1-C4 alkyl. In a further embodiment, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , 4 3 3 2 3 —S(=O) CH F, —S(=O) CHF , —S(=O) CF , —S(=O) NH , —S(=O) NHCH , 2 2 2 2 2 3 2 2 2 3 —S(=O)(=NH)CH , —S(=O)(=NH)CH F, —S(=O)(=NH)CHF , —S(=O)(=NH)CF , 3 2 2 3 —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, —S(=O)(=N-CN)CHF , and 3 2 2 —S(=O)(=N-CN)CF .

Described herein is a compound having the structure of Formula IIb or a pharmaceutically acceptable salt thereof, wherein: R2 is nitro, carboxaldehyde, carboxylic acid, ester, amido, cyano, halo, sulfonyl, or alkyl; R3 is hydrogen, halo, cyano, oxime, alkyl, heteroalkyl, alkenyl, alkynyl, alkylamino, or acyl; or R /R and atoms they are attached to form a 5- or 6-membered carbocycle with at least one sp hybridized carbon; R is nitro, halo, cyano, alkyl, sulfinyl, sulfonamide, sulfonyl, or sulfoximinyl; R is hydrogen, halo or alkyl; n is 1, 2, 3, or 4; and Rc is hydrogen, cyano, halo, alkyl or alkoxy.

In some embodiments, R is cyano, halo, or alkyl. In some embodiments, R is halo or alkyl. In some embodiments, R is fluoro, chloro, bromo, or iodo. In some embodiments, R is fluoroalkyl. In some further embodiments, R is —CH F, —CHF or 2 2 2 2 —CF .

In some embodiments, R is hydrogen, halo, cyano, alkyl, heteroalkyl, or acyl; or R /R and atoms they are attached to may optionally form a 5- or 6-membered carbocycle with at least one sp hybridized carbon. In a further embodiment, R is halo, cyano or alkyl.

In yet a further embodiment, R is —(CH ) OH, wherein n is 1, 2 or 3. 3 2 n In some embodiments, R /R and atoms they are attached to form a 5- or 6- membered carbocycle with at least one sp carbon. Representative compounds with the carbocycle include, but are not limited to, the following: wherein the carbocycle formed by linking R and R may be optionally substituted with fluoro, chloro, hydroxy, alkyl or heteroalkyl. In a further embodiment, the substituent(s) is selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R is hydrogen, R is —S(=O) R or 3 4 2 a —S(=O)(=NR )R , wherein R is fluoroalkyl, R is hydrogen, cyano or alkyl and R is alkyl. b d a b d In some embodiments, R is halo, cyano, fluoroalkyl, sulfinyl, sulfonamide, sulfonyl or sulfoximinyl. In some embodiments, R is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl or sulfoximinyl. In some embodiments, R is fluoroalkyl, sulfonamide, sulfonyl or sulfoximinyl.

In some embodiments, R is —S(=O) R , wherein R is alkyl or cycloalkyl. In 4 2 a a a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines.

Suitable examples of fluorine-substituted C1-C4 alkyl include, but are not limited to, — CH F, —CHF , —CF , —CH CF , —CH CHF , —CH CH F, —CHFCH , and —CF CH . In still a 2 3 2 3 2 2 2 2 3 2 3 further embodiment, R is methyl, optionally substituted with one or more fluorines.

In some embodiments, R is —S(=O)(=NR )R , wherein R is alkyl or 4 b a a cycloalkyl and R is hydrogen, cyano, or alkyl. In a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines. Suitable examples of fluorine-substituted C1-C4 alkyl include, but are not limited to, —CH F, —CHF , —CF , —CH CF , 2 2 3 2 3 —CH CHF , —CH CH F, —CHFCH , and —CF CH . 2 2 2 2 3 2 3 In some embodiments, R is —S(=O) —N(R ) , wherein each R is 4 2 a 2 a independently hydrogen, alkyl, heteroalkyl, cycloalkyl, or heterocycloalkyl; and at least one R is hydrogen. In a further embodiment, both R s are hydrogen. In another further embodiment, one R is hydrogen and the other R is C1-C4 alkyl.

In some embodiments, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , 3 3 2 3 2 2 2 2 2 3 —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 2 2 3 3 2 —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, 2 3 3 2 —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF .

In some embodiments, R is hydrogen. In some other embodiments, R is C1- C4 alkyl. In a further embodiment, R is methyl.

In some embodiments, R is —CH OH and R is fluoroalkyl, sulfonamide, 3 2 4 sulfonyl, sulfinyl, or sulfoximinyl. In a further embodiment, R is halo, cyano, or alkyl. In still a further embodiment, R is hydrogen.

In some embodiments, R is halo, cyano, or alkyl; R is —CH OH; R is 2 3 2 4 fluoroalkyl, sulfonamide, sulfinyl, sulfonyl, or sulfoximinyl; R is hydrogen; and R is halo, cyano, or alkyl. In a further embodiment, R is selected from the group consisting of —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , —S(=O) NH , 3 2 3 2 2 2 2 2 3 2 2 —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, —S(=O)(=NH)CHF , 2 3 3 2 2 —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, —S(=O)(=N-CN)CHF , 3 3 2 2 and —S(=O)(=N-CN)CF .

In some embodiments, R /R and atoms they are attached to form a 5- or 6- membered carbocycle with at least one sp carbon and R is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl, or sulfoximinyl. In a further embodiment, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , 3 3 2 3 2 2 2 2 —S(=O) CF , —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 3 2 2 2 3 3 2 —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH —S(=O)(=N-CN)CH F, 2 3 3, 2 —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF . In still a further embodiment, R is 2 3 5 hydrogen.

In some embodiments, Rc is cyano, halo, C1-C4 alkyl or C1-C4 alkoxy.

Described herein is a compound having the structure of Formula III (R ) n III, or a pharmaceutically acceptable salt thereof, wherein: n is 1, 2, 3 or 4; R is aryl or heteroaryl; R is nitro, halo, cyano, alkyl, sulfinyl, sulfonamide, sulfonyl, or sulfoximinyl; R is hydrogen, halo or alkyl; R is hydrogen, hydroxy, alkoxy, alkylamino, or amino; R is hydrogen, alkyl, alkenyl, or alkynyl, or R and R in combination form oxo or 9 8 9 oxime; and each of R is independently selected from the group consisting of hydrogen, fluoro, chloro, hydroxy, alkyl, and heteroalkyl with the proviso that when R is hydroxy, n is 1 or 2; or two R and the carbon atom(s) they are attached to form a 3- to 8-membered cycloalkyl or heterocycloalkyl.

In some embodiments, R is phenyl or monocyclic heteroaryl. In some further embodiments, R is phenyl or pyridyl, optionally substituted with one or more substituents selected from the group consisting of halo, alkyl, alkoxy, and cyano. In a further embodiment, R is wherein the aryl ring is optionally substituted with one or more substituents selected from the group consisting of cyano, halo, alkyl, and alkoxy. In another further embodiment, R is wherein X is N or CR , R is cyano, halo, alkyl, or alkoxy, and R is hydrogen, cyano, 7 6 7 halo, alkyl, or alkoxy.

In some embodiments, R is bicyclic heteroaryl.

In some embodiments, R is selected from the group consisting of: , and the rings specified for R may optionally be substituted with one or more substituents described for aryl and heteroaryl. In a further embodiment, the substituent(s) is selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R is cyano, fluoroalkyl, sulfinyl, sulfonamide, sulfonyl, or sulfoximinyl. In a further embodiment, R is fluoroalkyl, sulfonamide, sulfinyl, sulfonyl, or sulfoximinyl.

In some embodiments, R is —S(=O) R , wherein R is alkyl or cycloalkyl. In 4 2 a a a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines.

Suitable examples of fluorine-substituted C1-C4 alkyl include, but are not limited to, — CH F, —CHF , —CF , —CH CF , —CH CHF , —CH CH F, —CHFCH , and —CF CH . In still a 2 3 2 3 2 2 2 2 3 2 3 further embodiment, R is methyl, optionally substituted with one or more fluorines.

In some embodiments, R is —S(=O)(=NR )R , wherein R is alkyl or 4 b a a cycloalkyl and R is hydrogen, cyano, or alkyl. In a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines. Suitable examples of fluorine-substituted C1-C4 alkyl include, but are not limited to, —CH F, —CHF , —CF , —CH CF , 2 2 3 2 3 —CH2CHF2, —CH2CH2F, –CHFCH3, and –CF2CH3.

In some embodiments, R is —S(=O) —N(R ) , wherein each of R is 4 2 a 2 a independently hydrogen, alkyl, heteroalkyl, cycloalkyl, or heterocycloalkyl, and at least one R is hydrogen. In a further embodiment, both R s are hydrogen. In another further embodiment, one R is hydrogen and the other R is C1-C4 alkyl.

In some embodiments, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , 3 3 2 3 2 2 2 2 2 3 —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 2 2 3 3 2 —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, 2 3 3 2 —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF .

In some embodiments, R is hydrogen or alkyl. In some other embodiments, R is alkyl. In a further embodiment, R is C1-C4 alkyl.

In some embodiments, R is hydroxy or amino. In a further embodiment, R is hydroxy. In another further embodiment, R is amino.

In some embodiments, R is fluoro. In a further embodiment, n is 1, 2 or 3.

In some embodiments, R is monocyclic aryl or monocyclic heteroaryl and R is hydroxy or amino. In a further embodiment, R is fluoro. In still a further embodiment, n is 1, 2 or 3.

In some embodiments, R is phenyl or monocyclic heteroaryl, R is hydroxy or amino, R is fluoro, n is 1, 2 or 3 and R is hydrogen. 5 In some embodiments, R is bicyclic heteroaryl and R is hydroxy or amino. In a further embodiment, R is fluoro. In still a further embodiment, n is 1, 2 or 3.

In some embodiments, R is bicyclic heteroaryl, R is hydroxy or amino, R is 1 8 10 fluoro, n is 1, 2 or 3, and R is hydrogen.

In some embodiments, R is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl, or sulfoximinyl, and R is hydroxy or amino. In a further embodiment, R is hydrogen. In another further embodiment, R is fluoro. In still a further embodiment, n is 1, 2 or 3.

In some embodiments, R is cyano, fluoroalkyl, sulfonamide, sulfonyl, sulfinyl, or sulfoximinyl; R8 is hydroxy or amino; R10 is fluoro; n is 1, 2 or 3; and R5 is hydrogen. In a further embodiment, R is hydrogen.

In some embodiments, R8 is hydroxy or amino and R9 is hydrogen. In a further embodiment, R is fluoro. In still a further embodiment, n is 1, 2 or 3.

In some embodiments, R8 is hydroxy or amino, R9 is hydrogen, R10 is fluoro, n is 1, 2 or 3, and R is hydrogen. In a further embodiment, R is selected from the group consisting of —CN, —CF , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , 3 2 3 2 2 2 2 2 3 —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 2 2 3 3 2 —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, 2 3 3 2 —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF .

Described herein is a compound having the structure of Formula IVa, IVb, IVc or IVd: or a pharmaceutically acceptable salt thereof, wherein: R is aryl or heteroaryl; R is nitro, halo, cyano, alkyl, sulfinyl, sulfonamide, sulfonyl, or sulfoximinyl; R is hydrogen, halo or alkyl; and R is hydrogen, hydroxy, alkoxy, alkylamino or amino.

In some embodiments, R is monocyclic aryl or monocyclic heteroaryl. In some further embodiments, R is phenyl or pyridyl, optionally substituted with one or more substituents selected from the group consisting of halo, alkyl, alkoxy, and cyano. In a further embodiment, R is wherein the aryl ring may optionally be substituted with one or more substituents selected from the group consisting of cyano, halo, alkyl, and alkoxy. In another further embodiment, R is wherein X is N or CR , R is cyano, halo, alkyl or alkoxy, and R is hydrogen, cyano, 7 6 7 halo, alkyl, or alkoxy.

In some embodiments, R is bicyclic heteroaryl having at least one N atom.

In some embodiments, R is selected from the group consisting of: , and the rings specified for R may optionally be substituted by one or more substituents described for aryl and heteroaryl. In a further embodiment, the substituent(s) is selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R is cyano, fluoroalkyl, sulfinyl, sulfonamide, sulfonyl, or sulfoximinyl. In a further embodiment, R is fluoroalkyl, sulfonamide, sulfinyl, sulfonyl, or sulfoximinyl.

In some embodiments, R is —S(=O) R , wherein R is alkyl or cycloalkyl. In 4 2 a a a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines.

Suitable examples of fluoroalkyl include, but are not limited to, —CH F, —CHF , —CF , 2 2 3 —CH CF , –CH CHF , –CH CH F, –CHFCH , and –CF CH . In still a further embodiment, 2 3 2 2 2 2 3 2 3 R is methyl, optionally substituted with one or more fluorines.

In some embodiments, R is —S(=O)(=NR )R , wherein R is alkyl or 4 b a a cycloalkyl and R is hydrogen, cyano, or alkyl. In a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines. Suitable examples of fluoroalkyl include, but are not limited to, —CH2F, —CHF2, —CF3, —CH2CF3, —CH2CHF2, —CH2CH2F, —CHFCH , and —CF CH . 3 2 3 In some embodiments, R4 is —S(=O)2—N(Ra)2, wherein each Ra is independently hydrogen, alkyl, heteroalkyl, cycloalkyl, or heterocycloalkyl, and at least one R is hydrogen. In a further embodiment, both R s are hydrogen. In another further embodiment, one R is hydrogen and the other R is C1-C4 alkyl.

In some embodiments, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , 3 3 2 3 2 2 2 2 2 3 —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 2 2 3 3 2 —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, 2 3 3 2 —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF .

In some embodiments, R is hydrogen or alkyl. In some other embodiments, R is alkyl. In a further embodiments, R is C1-C4 alkyl.

In some embodiments, R is hydroxy. In some other embodiments, R is amino.

In some embodiments, R is bicyclic heteroaryl and R is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl, or sulfoximinyl. In a further embodiment, R is hydrogen. In another further embodiment, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , —S(=O) NH , 3 2 3 2 2 2 2 2 3 2 2 —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, —S(=O)(=NH)CHF , 2 3 3 2 2 —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, —S(=O)(=N-CN)CHF , 3 3 2 2 and —S(=O)(=N-CN)CF .

In some embodiments, R is bicyclic heteroaryl; R is cyano, fluoroalkyl, sulfonamide, sulfonyl, sulfinyl, or sulfoximinyl; R is hydroxy or amino; and R is hydrogen.

In a further embodiment, R is hydroxy. In another further embodiment, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, 3 3 2 3 2 2 —S(=O) CHF , —S(=O) CF , —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , 2 2 2 3 2 2 2 3 3 —S(=O)(=NH)CH F, —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , 2 2 3 3 —S(=O)(=N-CN)CH F, —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF . 2 2 3 In some embodiments, R is phenyl, or monocyclic heteroaryl and R is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl, or sulfoximinyl. In a further embodiment, R is hydrogen. In another further embodiment, R is selected from the group consisting of —CN, —CF3, —S(=O)CH3, —S(=O)2CH3, —S(=O)2CH2F, —S(=O)2CHF2, —S(=O)2CF3, —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 2 2 3 3 2 —S(=O)(=NH)CHF2, —S(=O)(=NH)CF3, —S(=O)(=N-CN)CH3, —S(=O)(=N-CN)CH2F, —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF .

In some embodiments, R1 is phenyl or monocyclic heteroaryl; R4 is cyano, fluoroalkyl, sulfonamide, sulfinyl, sulfonyl or sulfoximinyl; R is hydroxy or amino; and R is hydrogen. In a further embodiment, R is hydroxy. In another further embodiment, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , 3 3 2 3 —S(=O) CH F, —S(=O) CHF , —S(=O) CF , —S(=O) NH , —S(=O) NHCH , 2 2 2 2 2 3 2 2 2 3 —S(=O)(=NH)CH , —S(=O)(=NH)CH F, —S(=O)(=NH)CHF , —S(=O)(=NH)CF , 3 2 2 3 —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, —S(=O)(=N-CN)CHF , and —S(=O)(=N- 3 2 2 CN)CF .

In some embodiments, R is phenyl or monocyclic heteroaryl and R is hydroxy or amino. In a further embodiment, R is hydrogen. In another further embodiment, R is alkyl. In still a further embodiment, R is C1-C4 alkyl.

In some embodiments, R is bicyclic heteroaryl and R is hydroxy or amino. In a further embodiment, R is hydrogen. In another further embodiment, R is alkyl. In still a further embodiment, R is C1-C4 alkyl.

Described herein is a compound having the structure of Formula Va, Vb, Vc or Vd:: or a pharmaceutically acceptable salt thereof, wherein: R is aryl or heteroaryl; R is halo, cyano, alkyl, sulfonamide, sulfinyl, sulfonyl or sulfoximinyl; R is hydrogen, halo or alkyl; and R is hydroxy or amino.

In some embodiments, R is phenyl or monocyclic heteroaryl. In some further embodiments, R is phenyl or pyridyl, optionally substituted with one or more substituents selected from the group consisting of halo, alkyl, alkoxy, and cyano. In a further embodiment, R is wherein the aryl ring may optionally be substituted with one or more substituents selected from the group consisting of cyano, halo, alkyl, or alkoxy. In another further embodiment, R is wherein X is N or CR , R is cyano, halo, alkyl, or alkoxy, and R is hydrogen, cyano, 7 6 7 halo, alkyl, or alkoxy.

In some embodiments, R is bicyclic heteroaryl.

In some embodiments, R is selected from the group consisting of: , and the rings specified for R may optionally be substituted by one or more substituents described for aryl and heteroaryl. In a further embodiment, the substituent(s) is selected from the group consisting of halo, C1-C4 alkyl, C1-C4 alkoxy, and cyano.

In some embodiments, R is cyano, fluoroalkyl, sulfonamide, sulfonyl, sulfinyl, or sulfoximinyl.

In some embodiments, R is —S(=O) R , wherein R is alkyl or cycloalkyl. In 4 2 a a a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines.

Suitable examples of fluorine-substituted C1-C4 alkyl include, but are not limited to, — CH F, —CHF , —CF , —CH CF , —CH CHF , —CH CH F, —CHFCH , and —CF CH . In still a 2 3 2 3 2 2 2 2 3 2 3 further embodiment, R is methyl, optionally substituted with one or more fluorines.

In some embodiments, R is —S(=O)(=NR )R , wherein R is alkyl or 4 b a a cycloalkyl and R is hydrogen, cyano, or alkyl. In a further embodiment, R is C1-C4 alkyl, optionally substituted with one or more fluorines. Suitable examples of fluorine-substituted C1-C4 alkyl include, but are not limited to, —CH F, —CHF , —CF , —CH CF , 2 2 3 2 3 —CH CHF , —CH CH F, —CHFCH , and —CF CH . 2 2 2 2 3 2 3 In some embodiments, R is —S(=O) —N(R ) , wherein each R is 4 2 a 2 a independently hydrogen, alkyl, heteroalkyl, cycloalkyl, or heterocycloalkyl, and at least one R is hydrogen. In a further embodiment, both R s are hydrogen. In another further embodiment, one R is hydrogen and the other R is C1-C4 alkyl.

In some embodiments, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , 3 3 2 3 2 2 2 2 2 3 —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 2 2 3 3 2 —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, 2 3 3 2 —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF .

In some embodiments, R is hydrogen or alkyl. In some other embodiments, R is alkyl. In a further embodiments, R is C1-C4 alkyl.

In some embodiments, R is hydroxy. In some other embodiments, R is amino.

In some embodiments, R is bicyclic heteroaryl and R is cyano, fluoroalkyl, sulfonamide, sulfonyl, sulfinyl, or sulfoximinyl. In a further embodiment, R is hydrogen. In still a further embodiment, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , —S(=O) NH , 3 2 3 2 2 2 2 2 3 2 2 —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, —S(=O)(=NH)CHF , 2 3 3 2 2 —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, —S(=O)(=N-CN)CHF , 3 3 2 2 and —S(=O)(=N-CN)CF .

In some embodiments, R is bicyclic heteroaryl; R is cyano, fluoroalkyl, sulfonamide, sulfonyl, sulfinyl, or sulfoximinyl; R8 is hydroxy or amino; and R5 is hydrogen.

In a further embodiment, R is hydroxy. In still a further embodiments, R is selected from the group consisting of —CN, —CF3, —S(=O)CH3, —S(=O)2CH3, —S(=O)2CH2F, —S(=O) CHF , —S(=O) CF , —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , 2 2 2 3 2 2 2 3 3 —S(=O)(=NH)CH2F, —S(=O)(=NH)CHF2, —S(=O)(=NH)CF3, —S(=O)(=N-CN)CH3, —S(=O)(=N-CN)CH F, —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF . 2 2 3 In some embodiments, R is phenyl or monocyclic heteroaryl and R is cyano, fluoroalkyl, sulfonamide, sulfonyl, sulfinyl, or sulfoximinyl. In a further embodiment, R is hydrogen. In still a further embodiments, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , —S(=O) CH F, —S(=O) CHF , —S(=O) CF , 3 3 2 3 2 2 2 2 2 3 —S(=O) NH , —S(=O) NHCH , —S(=O)(=NH)CH , —S(=O)(=NH)CH F, 2 2 2 3 3 2 —S(=O)(=NH)CHF , —S(=O)(=NH)CF , —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, 2 3 3 2 —S(=O)(=N-CN)CHF , and —S(=O)(=N-CN)CF .

In some embodiments, R is phenyl or monocyclic heteroaryl; R is cyano, fluoroalkyl, sulfonamide, sulfonyl, sulfinyl, or sulfoximinyl; R is hydroxy or amino; and R is hydrogen. In a further embodiment, R is hydroxy. In still a further embodiments, R is selected from the group consisting of —CN, —CF , —S(=O)CH , —S(=O) CH , 3 3 2 3 —S(=O) CH F, —S(=O) CHF , —S(=O) CF , —S(=O) NH , —S(=O) NHCH , 2 2 2 2 2 3 2 2 2 3 —S(=O)(=NH)CH , —S(=O)(=NH)CH F, —S(=O)(=NH)CHF , —S(=O)(=NH)CF , 3 2 2 3 —S(=O)(=N-CN)CH , —S(=O)(=N-CN)CH F, —S(=O)(=N-CN)CHF , and —S(=O)(=N- 3 2 2 CN)CF .

In some embodiments, R is phenyl or monocyclic heteroaryl and R is hydroxy or amino. In a further embodiment, R is hydrogen. In another further embodiment, R is alkyl. In still a further embodiment, R is C1-C4 alkyl.

In some embodiments, R is bicyclic heteroaryl and R is hydroxy or amino. In a further embodiment, R is hydrogen. In another further embodiment, R is alkyl. In still a further embodiment, R is C1-C4 alkyl.

In some embodiments, a compound of any one of Formulae Va-Vd has enantiomeric excess of at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or even higher. In some embodiments, a compound of any one of Formulae Va-Vd has enantiomeric excess of about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99%.

The present disclosure provides and/or describes a compound or pharmaceutically acceptable salt selected from the group consisting of the following compounds: Example Number Structure Method of Use The chemical entities described herein are useful for the treatment, or in the preparation of a medicament for the treatment of HIF-2α mediated diseases, including but are not limited to, cancer. A role of HIF-2α in tumorigenesis and tumor progression has been implicated in many human cancers. One of the strongest links between HIF-2α activity and disease is in renal cell carcinoma (RCC), including clear cell renal cell carcinoma (ccRCC) (reviewed in Shen and Kaelin, Seminars in Cancer Biology 23: 18–25, 2013). Greater than eighty percent of ccRCC have defective VHL either through deletion, mutation or post- translational modification. Defective VHL in ccRCC results in constitutively active HIF-α proteins regardless of the oxygen level. A series of studies using gain-of-function and loss-of- function approaches in xenograft mouse models have clearly demonstrated that HIF-2α is the key oncogenic substrate of VHL (Kondo, et al. Cancer Cell 1: 237-246, 2002; Kondo, et al.

PLoS Biology 1: 439-444, 2002; Maranchi, et al. Cancer Cell 1: 247-255, 2002; Zimmer, et al. Mol. Cancer Res 2: 89–95, 2004). In these studies, biological knockdown of HIF-2α in VHL-null tumors inhibited tumor formation in a manner analogous to reintroduction of VHL.

And, overexpression of HIF-2α overcame the tumor suppressive role of VHL. In addition, single nucleotide polymorphism in HIF-2α that rendered HIF-2α refractory to PHD-mediated degradation have been linked to increased risk of kidney cancer. Furthermore, immunohistochemical analyses of morphologically normal renal tubular cells show HIF activation, thereby supporting an early, dominant pathologic role in the disease (Mandriota, et al. Cancer Cell 1: 459-468, 2002; Raval, et al. Mol. Cell. Biol. 25: 5675-5686, 2005). In addition to their role in tumor initiation, the VHL-HIF-2α axis has been implicated in ccRCC tumor metastasis (Vanharanta et al. Nature Medicine 19: 50-59, 2013). Genetic studies on HIF-1α have led to the hypothesis that HIF-1α acts as a tumor suppressor in kidney cancer.

HIF-1α resides on a frequently deleted chromosome in ccRCC and deletion of HIF-1α increased tumor growth in mice (reviewed in Shen and Kaelin, Seminars in Cancer Biology 23: 18– 25, 2013). Taken together, these data overwhelmingly support the potential therapeutic utility of HIF-2α targeted agents for the treatment of ccRCC.

VHL disease is an autosomal dominant syndrome that not only predisposes patients to kidney cancer (~70% lifetime risk), but also to hemangioblastomas, pheochromocytoma and pancreatic neuroendocrine tumors. VHL disease results in tumors with constitutively active HIF-α proteins with the majority of these dependent on HIF-2α activity (Maher, et al. Eur. J. Hum. Genet. 19: 617-623, 2011). HIF-2α has been linked to cancers of the retina, adrenal gland and pancreas through both VHL disease and activating mutations. Recently, gain-of-function HIF-2α mutations have been identified in erythrocytosis and paraganglioma with polycythemia (Zhuang, et al. NEJM 367: 922-930, 2012; Percy, et al. NEJM 358: 162-168, 2008; and Percy, et al. Am. J. Hematol. 87: 439-442, 2012). Notably, a number of known HIF-2α target gene products (e.g., VEGF, PDGF, and cyclin D1) have been shown to play pivotal roles in cancers derived from kidney, liver, colon, lung, and brain. In fact, therapies targeted against one of the key HIF-2α regulated gene products, VEGF, have been approved for the treatment of these cancers.

Due to poor vascularization, intratumor environment of rapidly growing tumors are normally hypoxic, a condition that activates HIF-α which supports tumor cell survival and proliferation. Studies have demonstrated a correlation between HIF-2α overexpression and poor prognosis in multiple cancers including astrocytoma, breast, cervical, colorectal, glioblastoma, glioma, head and neck, hepatocellular, non-small cell lung, melanoma, neuroblastoma, ovarian, and prostate, thereby providing support for HIF-2α as a therapeutic target for these diseases (reviewed in Keith, et al. Nature Rev. Cancer 12: 9-22, 2012). Also, epigenetic inactivation of VHL expression and thus constitutive activation of HIF-α proteins has been found in many cancers including RCC, multiple myeloma, retinoblastoma, NSCLC, pancreatic endocrine tumors, squamous cell carcinoma, acute myeloid leukemia, myelodysplastic syndrome, and esophageal squamous cell carcinoma (reviewed in Nguyen, et al. Arch. Pharm. Res 36: 252-263, 2013).

Specifically, HIF-2α has been demonstrated to play an important role in APC mutant colorectal cancer through control of genes involved in proliferation, iron utilization and inflammation (Xue, et al. Cancer Res 72: 2285-2293, 2012; and Xue and Shah, Carcinogenesis 32: 163-169, 2013). In hepatocellular carcinoma (HCC), knock-down of HIF- 2α in preclinical models reduced the expression of VEGF and cyclin D1 genes both in vitro and in vivo, resulting in inhibition of cell proliferation and tumor growth (He, et al. Cancer Sci. 103: 528-534, 2012). Additionally, fifty percent of NSCLC patients have overexpression of HIF-2α protein, which correlates strongly with VEGF expression and most importantly poor overall survival. HIF-1α is also overexpressed in many lung cancer patients. However, in contrast to HIF-2α, HIF-1α expression does not correlate with reduced overall survival (Giatromanolaki, et al. Br. J. Cancer 85: 881-890, 2001). In mice engineered with both non- degradable HIF-2α and mutant KRAS tumors, increased tumor burden and decreased survival were observed when compared to mice with only mutant KRAS expression (Kim, et al. J.

Clin. Invest. 119: 2160–2170, 2009). This research demonstrates that HIF-2α contributes to tumor growth and progression in lung cancer and suggests a relationship with clinical prognosis in NSCLC. Furthermore, HIF-2α activity has been linked to the progression of chronic obstructive pulmonary disease (COPD) and lung cancer in mouse models (Karoor, et al. Cancer Prev. Res. 5: 1061-1071, 2012). However, genetic deletion of HIF-2α in a KRAS mutant mouse model increased tumor growth through the reduction of Scgb3a1 tumor suppressor gene (Mazumdar, et al. PNAS 107: 14182-14187, 2010). In total, these studies implicate HIF-2α in lung cancer progression but suggest that maintenance of the basal HIF- 2α level maybe beneficial. HIF-2α activity has also been demonstrated to be important in central nervous system cancers (Holmquist-Mengelbier, et al. Cancer Cell 10: 413-423, 2006 and Li, et al. Cancer Cell 15: 501-513, 2009). In preclinical animal models of neuroblastoma, HIF-2α knockdown reduced tumor growth. Additionally, high protein levels of HIF-2α were correlated with advanced disease, poor prognosis and high VEGF levels. Similarly, poor survival in glioma correlated with HIF-2α expression. And, inhibition of HIF-2α in glioma stem cells reduced cell proliferation, and survival in vitro and tumor initiation in vivo.

Interestingly, while HIF-1α is expressed in both neural progenitors and brain tumor stem cells, HIF-2α is only expressed in the latter. Moreover, glioma survival is correlated to HIF- 2α but not HIF-1α levels.

Approximately 50% of cancer patients receive radiation treatment, either alone or in combination with other therapies. Tumor hypoxia has long been associated with resistance to radiation therapy. Therefore, inhibition of HIF-2α could improve radiation response of cancer/tumor cells. Bhatt and co-workers showed that decreasing levels of HIF- 2α leads to increased sensitivity to ionizing radiation in renal cell carcinoma cell lines (Bhatt, et al. BJU Int. 102: 358-363, 2008). Furthermore, Bertout and co-workers demonstrated that HIF-2α inhibition enhances effectiveness of radiation through increased p53-dependent apoptosis (Bertout, et al. PNAS 106: 14391-14396, 2009).

Multiple groups have reported attempts to discover inhibitors of HIF-α activity. These efforts include irreversible inhibitors, small molecules, cyclic peptides and natural products (Cardoso, et al. Protein Sci. 21: 1885-1896, 2012, Miranda, et al. 2013, Mooring, et al. J. Am. Chem. Soc. 135: 10418-10425, 2011, Tan, et al. Cancer Res. 65: 605- 612, 2005, and WO2013011033 and WO2013057101). Some indirect, non-specific approaches to block HIF-α protein activity have also been described (Zimmer, et al. Mole Cell 32: 838-848, 2008 and Carew, et al. PLoS ONE 7: e31120, 2012). The reported molecular mechanisms of these approaches include decreased HIF-1α mRNA levels, decreased HIF-1α protein synthesis, increased HIF-1α degradation, decreased HIF subunit heterodimerization, decreased HIF binding to DNA, and decreased HIF transcriptional activity. For example, acriflavine, an antibacterial agent, is reported to bind directly to the PAS-B domain of HIF-1α and HIF-2α and block their interaction with HIF-1β, thereby blocking HIF-dependent gene transcription and leading to impaired tumor growth and vascularization (Lee, et al. PNAS 106: 17910-17915, 2009). Furthermore, HIF-1α protein synthesis has reported to be blocked by various molecules including rapamycin, temsirolimus, everolimus, cardiac glycosides, microtubule targeting agents (taxotere), and topoisomerase inhibitors (topotecan). Drugs that induce degradation of HIF-1α include HSP90 inhibitors, e.g., 17-allylaminodemethoxygeldanamycin, and antioxidants, such as ascorbate. Anthracyclines, such as doxorubicin and daunorubicin, bind to DNA and block the binding of HIF-1α and HIF-2α in cultured cells and also block HIF-1α -dependent expression of angiogenic growth factors, leading to impaired tumor growth (Semenza, Trends Pharmacol. Sci. 33: 207-214, 2012). However, attempts to identify selective molecules that directly interfere with HIF-2α function have been met with little success, evidenced by the current paucity of clinical (or pre-clinical) programs targeting this transcription factor.

Recent work from Professors Kevin Gardner and Richard Bruick at the University of Texas Southwestern Medical Center has revealed a unique ligand-binding pocket in a select domain of HIF-2α that is required for HIF-2α transcriptional activity. High- resolution structural data gathered against one of the isolated HIF-2α PAS domains, both alone and in complexes, revealed a large internal hydrated cavity (280 A ) -- highly unusual for a protein of this size (Scheuermann et al. PNAS 106: 450-455, 2009 and Key et al. J. Am.

Chem. Soc., 131: 17647-17654, 2009). Furthermore, small molecule HIF-2α PAS B domain binders have been identified (Rogers, et al. J. Med. Chem. 56: 1739-1747, 2013). Binding of these ligands leads to inhibition of HIF-2α transcriptional activity in cells (Scheuermann, et al. Nat Chem Biol. 9: 271-276, 2013).

The compounds or their pharmaceutical compositions described herein are useful as inhibitors of HIF-2α. Thus, without wishing to be bound by any particular theory, the compounds or their pharmaceutical compositions described herein are particularly useful for treating or lessening the severity of a disease, condition, or disorder where activation of HIF-2α and/or one or more downstream processes associated with the activation or over activation of HIF-2α are implicated in the disease, condition, or disorder. Accordingly, described herein is a method for treating or lessening the severity of a disease, condition, or disorder where activation or over activation of HIF-2α is implicated in the disease state.

Described herein is a method of treating renal cell carcinoma of a subject with a compound described herein or a pharmaceutically acceptable salt thereof. RCC is one of the most common forms of kidney cancer arising from the proximal convoluted tubule. RCC is also known as hypernephroma. Initial treatment is commonly a radical or partial nephrectomy and remains the mainstay of curative treatment. Where the tumor is confined to the renal parenchyma, the 5-year survival rate is 60-70%, but this is lowered considerably where metastasis have spread. RCC is generally resistant to radiation therapy and chemotherapy, although some cases respond to immunotherapy. Targeted cancer therapies such as sunitinib, temsirolimus, bevacizumab, axitinib, pazopanib, interferon-alpha, and sorafenib have improved the outlook for RCC (progression-free survival), although they have not yet demonstrated improved survival rate. Subtypes of RCC include, but are not limited to, clear cell renal cell carcinoma, papillary renal cell carcinoma, and chromophobe renal cell carcinoma.

Pharmaceutical Compositions and Dosage Forms A compound or a pharmaceutically acceptable salt thereof may be formulated as a pharmaceutical composition prior to being administered to a subject. The pharmaceutical composition may comprise additional additives such as pharmaceutically acceptable excipients, carriers, and vehicles. Suitable pharmaceutically acceptable excipients, carriers, and vehicles include but are not limited to processing agents and drug delivery modifiers, for example, ethylene glycol, calcium phosphate, magnesium stearate, talc, monosaccharides, disaccharides, starch, gelatin, cellulose, methyl cellulose, hydroxypropyl cellulose, sodium carboxymethyl cellulose, dextrose, hydroxypropyl-β-cyclodextrin, polyvinylpyrrolidine, low melting waxes, ion exchange resins, and the like, as well as combinations of any two or more thereof.

A pharmaceutical composition comprising a compound or a pharmaceutically acceptable salt thereof may be administered enterally, orally, parenterally, sublingually, rectally, or topically in a unit dosage containing pharmaceutically acceptable excipients, carriers, or vehicles. Generally, the unit dosage is a dose sufficient for the compound or its pharmaceutically acceptable salt to achieve desired therapeutic effect. Suitable modes of administration include oral, subcutaneous, intra-arterial, intramuscular, intraperitoneal, intranasal, intraocular, subdural, vaginal, gastrointestinal, and the like. The compound or its salt can also be administered as prodrugs, wherein the prodrugs undergo transformation in the body of the treated subject to form a therapeutically active ingredient.

A pharmaceutical composition comprising a compound or a pharmaceutically acceptable salt described herein may be in any form suitable for the intended purpose of administration, including, for example, a solid or a liquid dosage form. The liquid dosage form may include solution, suspension, softgel, syrup, elixir, or emulsion. Liquid carriers are typically used in preparing solutions, suspensions, and emulsions. Liquid carriers contemplated for use in the practice of the present invention include, for example, water, saline, ethylene glycol, propylene glycol, pharmaceutically acceptable organic solvents, pharmaceutically acceptable oils or fats, and the like, as well as mixtures of two or more thereof. The liquid carrier may contain other suitable pharmaceutically acceptable additives such as solubilizers, emulsifiers, nutrients, buffers, preservatives, suspending agents, thickening agents, viscosity regulators, stabilizers, and the like. Suitable organic solvents include, for example, monohydric alcohols, such as ethanol, and polyhydric alcohols, such as glycols. Suitable oils include, for example, soybean oil, coconut oil, olive oil, safflower oil, cottonseed oil, sunflower oil, and the like. For parenteral administration, the carrier can also be an oily ester such as isopropyl myristate, and the like. Compositions of the present invention may also be in the form of nanoparticles, microparticles, microcapsules, liposomal encapsulates, and the like, as well as combinations of any two or more thereof. Solid dosage forms for oral administration may include capsule, tablet, pill, powder, and granule. In such solid dosage forms, the active compound may be admixed with at least one inert diluent such as sucrose, lactose, or starch. Such dosage forms may also comprise additional substances other than inert diluents, e.g., lubricating agents such as magnesium stearate. In the case of capsules, tablets, and pills, the dosage forms may also comprise buffering agents. Tablets and pills can additionally be prepared with enteric coatings.

In cases of a solid dosage form, examples of daily dosages of the compounds described herein which can be used are an effective amount within the dosage range of about 0.001 mg to about 2 mg per kilogram of body weight, about 0.001 mg to about 5 mg per kilogram of body weight, about 0.001 mg to about 10 mg per kilogram of body weight, about 0.001 mg to about 20 mg per kilogram of body weight, about 0.001 mg to about 50 mg per kilogram of body weight, about 0.001 mg to about 100 mg per kilogram of body weight, about 0.001 mg to about 200 mg per kilogram of body weight, or about 0.001 mg to about 300 mg per kilogram of body weight. When administered orally or by inhalation, examples of daily dosages are an effective amount within the dosage range of about 0.1 mg to about 10 mg, or about 0.1 mg to about 20 mg, or about 0.1 mg to about 30 mg, or about 0.1 mg to about 40 mg, or about 0.1 mg to about 50 mg, or about 0.1 mg to about 60 mg, or about 0.1 mg to about 70 mg, or about 0.1 mg to about 80 mg, or about 0.1 mg to about 90 mg, or about 0.1 mg to about 100 mg, or about 0.1 mg to about 200 mg, or about 0.1 mg to about 300 mg, or about 0.1 mg to about 400 mg, or about 0.1 mg to about 500 mg, or about 0.1 mg to about 600 mg, or about 0.1 mg to about 700 mg, or about 0.1 mg to about 800 mg, or about 0.1 mg to about 900 mg, or about 0.1 mg to about 1 g, or about 20 mg to 300 mg, or about 20 mg to 500 mg, or about 20 mg to 700 mg, or about 20 mg to 1000 mg, or about 50 mg to 1500 mg, or about 50 mg to 2000 mg. Preferred fixed daily doses include about 1 mg, about 2 mg, about 3 mg, about 4 mg, about 5 mg, about 6 mg, about 7 mg, about 8 mg, about 9 mg, about mg, about 12 mg, about 15 mg, about 18 mg, about 20 mg, about 30 mg, about 40 mg, about 50 mg, about 60 mg, about 70 mg, about 80 mg, about 90 mg, about 100 mg, about 150 mg, about 200 mg, about 250 mg, about 300 mg, about 400 mg, about 500 mg, about 600 mg, about 700 mg, about 800 mg, about 900 mg, about 1000 mg, about 1200 mg, about 1500 mg, or about 2000 mg, independently of body weight. However, it is understood that pediatric patients may require smaller dosages, and depending on the severity of the disease and condition of the patient, dosages may vary. The compound will preferably be administered once daily, but may be administered two, three or four times daily, or every other day, or once or twice per week.

When formulated as a liquid, the concentration of the compounds described herein may be about 0.01 mg/ml to about 0.1 mg/ml or about 0.1 mg/ml to about 1 mg/ml, but can also be about 1 mg/ml to about 10 mg/ml or about 10 mg/ml to about 100 mg/ml. The liquid formulation could be a solution or a suspension. When formulated as a solid, for example as a tablet or as a powder for inhalation, the concentration, expressed as the weight of a compound divided by total weight, will typically be about 0.01% to about 0.1%, about 0.1% to about 1%, about 1% to about 10%, about 10% to about 20%, about 20% to about 40%, about 40% to about 60%, about 60% to about 80%, or about 80% to about 100%.

The compounds of the present invention can also be administered in the form of liposomes. As is known in the art, liposomes are generally derived from phospholipids or other lipid substances. Liposomes are formed by mono- or multilamellar hydrated liquid crystals that are dispersed in an aqueous medium. Any non-toxic, physiologically acceptable and metabolizable lipid capable of forming liposomes can be used. The present compositions in liposome form can contain, in addition to a compound of the present invention, stabilizers, preservatives, excipients, and the like. The preferred lipids are the phospholipids and phosphatidyl cholines (lecithins), both natural and synthetic. Methods to form liposomes are known in the art. See, for example, Prescott, Ed., “Methods in Cell Biology”, Volume XIV, ISBN: 978122, Academic Press, New York, N.W., p. 33 (1976) and Medina, Zhu, and Kairemo, “Targeted liposomal drug delivery in cancer”, Current Pharm. Des. 10: 2981-2989, 2004. For additional information regarding drug formulation and administration, see “Remington: The Science and Practice of Pharmacy,” Lippincott Williams & Wilkins, Philadelphia, ISBN-10: 0781746736, 21 Edition (2005).

Method of Making Compounds disclosed herein may be prepared by routes described below.

Materials used herein are either commercially available or prepared by synthetic methods generally known in the art. These schemes are not limited to the compounds listed or by any particular substituents, which are employed for illustrative purposes. Although various steps are described and depicted in Schemes 1-12, the steps in some cases may be performed in a different order than the order shown. Various modifications to these synthetic reaction schemes may be made and will be suggested to one skilled in the art having referred to the disclosure contained in this Application. Numberings or R groups in each scheme do not necessarily correspond to that of claims or other schemes or tables.

Scheme 1 In some embodiments, compounds of Formula 1-9 are prepared according to steps outlined in Scheme 1. The synthesis starts with phenol 1-1. Reaction of 1-1 with chloride 1-2 (wherein R and R are independently alkyl) provides intermediate 1-3. The reaction may be carried out in a suitable organic solvent in the presence of a base. Suitable bases for the reaction include, but are not limited to, organic bases, for example, triethylamine, N,N-diisopropylethylamine, 1,4-diazabicyclo[2.2.2]octane, and inorganic bases, for example, sodium hydroxide, cesium carbonate, cesium bicarbonate, sodium carbonate, and potassium carbonate. Compound 1-3 is then subjected to a rearrangement reaction to give compound 1-4. Elevated temperature may be needed for the rearrangement to occur. The temperature may be in a range of 100 C to 300 C. In some embodiments, the temperature is in a range of 180 C to 240 C. Hydrolysis of compound 1-4 provides thiophenol 1-5, which is alkylated to provide compound 1-6. A variety of alkyl group may be introduced. In some embodiments, R is a C1-C4 alkyl. In a further embodiment, R is a C1- C4 fluoroalkyl. Oxidation of compound 1-6 may be accomplished by a variety of methods known in the art, including but are not limited to, RuCl catalyzed oxidation in the presence of NaIO , oxidation with m-chloroperbenzoic acid (mCPBA) and oxidation with Oxone .

The ketone in 1-7 is then reduced to give alcohol 1-8, which then undergoes a nucleophilic aromatic substitution (SNAr) reaction with a suitable substrate R OH (wherein R is aryl or heteroaryl) to give compounds of Formula 1-9. Temperature for carrying out the SNAr reaction may depend on the reactivity of both R OH and/or compound 1-8. The reaction may be carried out in a temperature range from room temperature to 200 C. In some embodiments, the temperature range is from room temperature to 60 C. In some other embodiments, the temperature range is from 60 C to 100 C. In some other embodiments, the temperature range is from 100 C to 200 C.

Scheme 2 In some other embodiments, compounds of Formula 1-9 are prepared asymmetrically to give compounds of Formula 2-2 (Scheme 2). For example, direct asymmetric reduction of ketone 1-7 (Step A) may be accomplished chemically or enzymatically. For a recent review on enzymatic reduction of ketones, see Moore, et al. Acc.

Chem. Res. 40: 1412–1419, 2007. Examples of chemical asymmetric reduction of ketone include, but are not limited to, Corey-Bakshi-Shibata (CBS) reduction, asymmetric hydrogenation, and asymmetric transfer hydrogenation. In some embodiments, the asymmetric transfer hydrogenation is catalyzed by ruthenium. For examples of methods and catalysts for ruthenium catalyzed transfer hydrogenation, see US patents 6,184,381 and 6,887,820. Exemplary catalysts for asymmetric transfer hydrogenation include, but are not limited to, the following (shown as the R, R configuration): The asymmetric transfer hydrogenation may be carried out at or below room temperature. In some embodiments, the asymmetric transfer hydrogenation is carried out at about 4 C. The alcohol product may have an enantiomeric excess of at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, or even higher. It is well understood by one skilled in the art that changing the catalyst configuration will lead to a product with the opposite configuration. The chiral alcohol 2-1 can be coupled with a suitable substrate, for example a phenol, to give compounds of Formula 2-2 without significant loss of enantiomeric excess. The loss of enantiomeric excess (ee) in the coupling step for 2-2 may be less than about 1%, less than about 2%, less than about 3%, less than about 4%, less than about 5%, less than about 6%, or less than about 8%.

Scheme 3 In some embodiments, compounds of Formula 3-6 are prepared according to Scheme 3. The ketone in 1-7 is protected as a ketal to give compound 3-1, wherein each of R and R is independently an alkyl group. In addition, R and R may optionally be connected 4 5 to form a cyclic ketal. Exemplary structures of ketal 3-1 include, but are not limited to, the following: Ketal 3-1 and a suitable a suitable substrate R OH (wherein R is aryl or heteroaryl) may undergo a nucleophilic aromatic substitution reaction (SNAr) to give biaryl ether 3-2. Similarly to the SNAr reaction described in Step G of Scheme 1, the reaction temperature may depend on the reactivity of ketal 3-1 and/or R OH. Following deprotection of the ketal in 3-2, the resulting ketone 3-3 is condensed with an amine to form imine 3-4, wherein R is alkyl. The imine functional group in 3-4 may exist as a mixture of E, Z isomers. Fluorination of 3-4 can be accomplished with a fluorinating reagent, for example, 1- (chloromethyl)fluoro-1,4-diazoniabicyclo[2.2.2]octane ditetrafluoroborate, to give difluoroketone 3-5 after acid hydrolysis. Finally, reduction of the ketone in 3-5 with a hydride donor gives compounds of Formula 3-6.

Scheme 4 Similarly, compounds of Formula 4-1 can be prepared in asymmetric fashion by asymmetric reduction as outlined in Scheme 2. In some embodiments, the asymmetric reduction gives compounds of Formula 4-1 with an enantiomeric excess of at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98% or even higher. The enantiomeric excess of compounds of Formulae 2-2 and 4-1 may be determined by chrial HPLC or Mosher ester analysis. For determination of ee with Mosher ester, see Hoye, et al. Natural Protocol, 2: 2451, 2007.

Scheme 5 Alternatively, compounds of Formula 4-1 are prepared according to Scheme . The ketone in 5-1 is fluorinated to give monofluoroketone 5-2, which is then converted to a silylenol ether, e.g., TBS enol ether 5-3. Other silyl protecting groups, for example, triisopropylsilyl or diphenyl-t-butylsilyl, may also be used. The resulting enol ether is further fluorinated to give difluoroketone 5-4, which undergoes an asymmetric reduction, such as asymmetric transfer hydrogenation as described herein, to give chiral alcohol 5-5. Protection of the hydroxy moiety, followed by SNAr reaction and then deprotection provides compounds of Formula 4-1.

Scheme 6 Alternatively, compounds of Formula 3-6 are prepared according to Scheme 6.

Treatment of aryl fluoro 3-1 with a hydroxide source gives phenol 6-1. Suitable hydroxide sources include, but are not limited to, sodium hydroxide and potassium hydroxide. Suitable solvents for the reaction include, but are not limited to, DMSO, DMA, DMF or EtOH. The phenol 6-1 can react with an aryl or heteroaryl halide via a SNAr reaction to give biaryl ether 3-2, which can be converted to compounds of Formula 3-6 as described in Scheme 3.

Scheme 7 Compounds of Formula 7-3 and 7-4 may be prepared according to Scheme 7.

For example, condensation of NH R with difluoroketone 7-1, wherein R is aryl or 2 3 1 heteroaryl and R is aryl, heteroaryl, alkyl, heteroalkyl, heterocycle, or cycloalkyl, gives intermediate 7-2. In some embodiments, R is a chiral auxiliary. Exemplary chiral auxiliaries include but are not limited to the following: and their enantiomers thereof. Hydride reduction of intermediate 7-2 yields 7-3. At this stage, the chiral auxiliary may be cleaved under appropriate conditions, e.g., hydrogenation or acid treatment, to give chiral secondary amine 7-4. In some other embodiments, when compounds of Formula 7-3 are desirable, wherein R is not hydrogen, asymmetric hydrogenation or asymmetric transfer hydrogenation is applied on intermediate 7-2 to give compounds of Formula 7-3. For a review on asymmetric hydrogenation and asymmetric transfer hydrogenation, see Iwao Ojima ed. Catalytic Asymmetric Synthesis, Wiley-VCH, Inc., 2000, ISBN 029805-0.

Scheme 8 In some embodiments, compounds of Formula 8-2 are prepared according to Scheme 8. For example, ketones of Formula 3-3 is monofluorinated to give monofluoroketones of Formula 8-1. The monofluorination can be acheived with a variety of fluorinating reagents, e.g., N-Fluoro-o-benzenedisulfonimide, acetyl hypofluorite, ® ® ® Accufluor , Selectluor , Selectfluor II, or N-Fluorobenzenesulfonimide, in the presence or absence of a base. The compounds of Formula 8-1 are reduced to give compounds of Formula 8-2. In some cases, the reduction is highly diasteroselective to give compounds of Formula 8-2 with greater than 80%, greater than 82%, greater than 84%, greater than 86%, greater than 88%, greater than 90%, greater than 92%, greater than 94%, greater than 96%, or even greater than 96% diasteroselectivity. In some cases, the reduction is highly enantioselective to give compounds of Formula 8-2 with greater than 80%, greater than 82%, greater than 84%, greater than 86%, greater than 88%, greater than 90%, greater than 92%, greater than 94%, greater than 96%, or even greater than 96% enantioselectivity. Reduction conditions to achieve high enantioselectivity include, but are not limited to, asymmetric transfer hydrogenation and enzymatic reduction as described herein.

Scheme 9 In some embodiments, compounds of Formula 9-6 are prepared according to scheme 9, wherein R is hydrogen, alkyl or fluoro. The hydroxy group in compounds of Formula 9-1 may be protected with, e.g., acyl or methoxymethyl ether (MOM), to give compounds of Formula 9-2. Benzylic bromination in Step B may be carried out with a bromide source, e.g., N-bromosuccinimide, in the presence of a radical initiator, e.g., 2,2’- azobis(2-methylpropionitrile) (AIBN) or benzyol peroxide. The bromide in compounds of Formula 9-3 can be replaced with a hydroxy group in a solvent comprising water in the presence of a silver salt, e.g., Ag CO or AgClO or AgBF . Finally, fluorination of the 2 3 4 4 hydroxy group in Formula 9-4 followed by deprotection gives compounds of Formula 9-6. In some cases, direct benzylic oxidation may be used for converting compounds of Formula 9-2 to compounds of Formula 9-4, thus bypassing an intermediate bromination step.

Scheme 10 In some embodiments, compounds of Formula 10-7 is prepared according to Scheme 10. For example, compounds of Formula 10-3 may be prepared from compounds of Formula 3-2 by following a similar sequence as outlined in Scheme 9. Further functional group manupilations lead to compounds of Formula 10-7.

Scheme 11 Alternatively, compounds of Formula 10-3 is deprotected to give diketone 11- 1, which is fluorinated to give difluoro diketone 11-2. Asymmetric reduction of 11-2 provides diol 11-2. In some embodiments, one of the hydroxy groups is selectively fluorinated to give compounds of Formula 10-7.

Scheme 12 Alternatively, compounds of Formula 10-7 are prepared according to Scheme 12. For example, difluoroketone 12-2 is reduced to give hydroxyketone 12-3. The reduction maybe enantioselective under transfer hydrogenation conditions with a Ru-catalysis as described herein. One of the aryl fluorine may be selective displaced with an alkyl thiol to give compounds of Formula 12-4. Oxidation, fluorination, followed by nucleophilic aromatic substitution give compounds of Formula 10-7.

Scheme 13 In some embodiments, compounds of Formula 13-4 are prepared according to Scheme 13. Aryl sulfides 13-1 are treated with H N-R and an oxidant, e.g., diacetoxyiodobenzene or dipivaloyloxyiodobenzene, in a suitable solvent, such as acetoniltrile, to obtain aryl sulfinimides 13-2. In some embodiments, for compounds of Formula 13-1 with fluoroalkyl R substituents, the presence of rhodium(II) acetate or Rh (esp) catalyst, along with magnesium oxide, is helpful. Oxidation of the aryl sulfinimides 13-2 to substituted sulfoximines 13-3 may be accomplished with catalytic ruthenium(III) chloride and sodium periodate in a suitable solvent, such as a mixture of water, acetonitrile, and carbon tetrachloride. Substituted sulfoximines 13-3 are then manipulated similarly as described in Schemes 3 and 4 to afford sulfoximines of Formula 13-4 as a diastereomeric mixture. The diastereomers may be separated by column chromatography.

Experiments The examples below are intended to be purely exemplary and should not be considered to be limiting in any way. Efforts have been made to ensure accuracy with respect to numbers used (for example, amounts, temperature, etc.) but some experimental errors and deviations should be taken into account. 1 19 H and F NMR analysis of intermediates and exemplified compounds were performed on an Agilent Technologies 400/54 magnet system (operating at 399.85 MHz or 376.24 MHz). Vnmrj VERSION 3.2 software Pulse sequences were selected from the default experiment set. Reference frequency was set using TMS as an internal standard. Typical deuterated solvents were utilized as indicated in the individual examples.

LCMS analysis of intermediates and exemplified compounds was performed on an Agilent Technologies 1200 Series HPLC system coupled to an Agilent Technologies 6150 Quadrapole LC/MS detector. Analytes were detected by UV absorbance at 220 and 254 nm. Analyte ions were detected by mass spectrometry in both negative and positive modes (110 – 800 amu scan range, API-ES ionization). A long HPLC method was run on a Phenomenex Kinetex 2.6 μm C18 100Å, 30 x 3.00 mm column. The column temperature was set at 40 °C. UV absorptions were detected at 220 and 254 nm. Samples were prepared as a solution in about 1:1 (v/v) acetonitrile:water mixture. Flow rate was about 0.80 mL/minute. Elution solvents were acetonitrile and water each containing 0.1% formic acid. In a typical run, a linear gradient starting with 5% acetonitrile and 95% water and ending with 95% acetonitrile and 5% water over 12 minutes was carried out. At the end of each run, the column was washed with 95% acetonitrile and 5% water for 2 minutes.

Enantiomeric excess was determined by Mosher ester analysis or with chiral HPLC. The chiral HPLC analysis was performed on an Agilent Technologies 1200 Series HPLC system. Analytes were detected by UV absorbance at 220 and 254 nm. A detailed description of the analytical method is provided below: Column: Lux® 5u Cellulose-4 5.0 μm 1000 Å, 150 x 4.60 mm Flow rate: 1.5 mL/min Mobile phase A: 0.1% Formic acid in water Mobile phase B: 0.1% Formic acid in Acetonitrile Strong needle wash: 90% Acetonitrile, 10% Water Weak needle wash: 10% Water, 90% Acetonitrile Injection volume: 2 µL Column temperature: 40 °C Autosampler temperature: Room temperature Run time: 5.0 min Gradient: 60% mobile phase A and 40% moble phase B Routine chromatographic purification was performed using Biotage Isolera One automated systems running Biotage Isolera One 2.0.6 software (Biotage LLC, Charlotte, NC). Flow rates were the default values specified for the particular column in use. Reverse phase chromatography was performed using elution gradients of water and acetonitrile on KP-C18-HS Flash+ columns (Biotage LLC) of various sizes. Typical loading was between 1:50 and 1:1000 crude sample : RP SiO by weight. Normal phase chromatography was performed using elution gradients of various solvents (e.g. hexane, ethyl acetate, methylene chloride, methanol, acetone, chloroform, MTBE, etc.). The columns were SNAP Cartridges containing KP-SIL or SNAP Ultra (25 μm spherical particles) of various sizes (Biotage LLC). Typical loading was between 1:10 to 1:150 crude sample : SiO by weight.

Compound names were generated with ChemBioDraw ultra 13.0.0.3015 or OpenEye Scientific Software’s mol2nam application.

Example 1 (R)(3-chlorofluorophenoxy)((difluoromethyl)sulfonyl)-2,3-dihydro- 1H-indenol (Compound 1) Step A: Preparation of O-(7-fluorooxo-indanyl)-N,N- dimethylcarbamothioate: A mixture of 4-fluorohydroxy-indanone (17.0 g, 102 mmol), DMF (340 mL), N,N-dimethylcarbamothioyl chloride (37.9 g, 307 mmol), and 1,4- diazabicyclo[2.2.2]octane (34.4 g, 307 mmol) was stirred at ambient temperature for 2 hours.

The reaction was poured into cold water and extracted with EtOAc. The combined organic layers were washed with water and brine, dried and concentrated. The resulting solid was recrystallized from 1:1 hexane:EtOAc (240 mL) to give O-(7-fluorooxo-indanyl)-N,N- dimethylcarbamothioate as a white solid (12.0 g). The mother liquid was concentrated and purified by flash chromatography on silica gel (0-1% EtOAc in dichloromethane) to give a solid, which was triturated with 4:1 hexane:EtOAc to give additional O-(7-fluorooxo- indanyl)-N,N-dimethylcarbamothioate (6.9 g, combined yield 18.9 g, 73%). LCMS ESI (+) m/z 254 (M+H).

Step B: Preparation of S-(7-fluorooxo-indanyl)-N,N- dimethylcarbamothioate: A mixture of O-(7-fluorooxo-indanyl)-N,N- dimethylcarbamothioate (18.9 g, 74.6 mmol) and diphenyl ether (200 mL) was heated at 220 C under nitrogen for 30 minutes. After cooling, the reaction mixture was diluted with hexane. The mixture was passed through a short silica gel pad eluting with hexane to remove diphenyl ether. Further elution with EtOAc afforded the crude product, which was purified by flash chromatography on silica gel (15-40% EtOAc/hexane) to afford S-(7-fluorooxo- indanyl)-N,N-dimethylcarbamothioate (18.0 g, 95%) as a solid. LCMS ESI (+) m/z 254 (M+H).

Step C: Preparation of 4-fluorosulfanyl-indanone : A stirred mixture of S-(7-fluorooxo-indanyl)-N,N-dimethylcarbamothioate (25.0 g, 98.7 mmol), 95% ethanol (490 mL) and 3N NaOH (173 mL, 691 mmol) was heated under nitrogen at reflux for minutes. After cooling, the reaction mixture was cooled to 0 C using an ice bath. 3N HCl was added dropwise to adjust the pH to 4-5. Most ethanol was evaporated under reduced pressure. The precipitated solid was collected by filtration, washed with water and dried to give 4-fluorosulfanyl-indanone (17.0 g, 95%), which was used in the next step without further purification.

Step D: Preparation of 7-(difluoromethylsulfanyl)fluoro-indanone : To a stirred solution of 4-fluorosulfanyl-indanone (crude from Step C, 17.0 g, 93.3 mmol) in acetonitrile (490 mL) was added a solution of KOH (104.7 g, 1866 mmol) in water (490 mL).

The reaction mixture was purged with nitrogen and then cooled to -78 C. Bromodifluoromethyl diethylphosphonate (33.2 mL, 187 mmol) was added all in once.

The resulting mixture was allowed to warm to ambient temperature and vigorously stirred for 2 hours. The reaction mixture was partitioned between EtOAc and water. The aqueous layer was extracted with EtOAc. The combined organics were washed with water and brine, dried over Na SO , filtered, and concentrated to dryness. The residue was purified by passing through a short silica gel pad eluting with 10% EtOAc in hexane to give 7- (difluoromethylsulfanyl)fluoro-indanone (18.3 g, 84%), which was used in the next step without further purification. LCMS ESI (+) m/z 233 (M+H).

Step E: Preparation of 7-((difluoromethyl)sulfonyl)fluoro-2,3-dihydro-1H- indenone: Sodium periodate (41.9 g, 196 mmol) was added all at once to 7- (difluoromethylsulfanyl)fluoro-indanone (18.2 g,78.4 mmol) and ruthenium(III) chloride (0.41 g, 2.0 mmol) in acetonitrile (392 mL) / carbon tetrachloride (392 mL) / water (392 mL) . The reaction mixture was stirred at ambient temperature for 5 hours. Solids were removed by filtration through Celite and rinsed with CH Cl . The organic layer was separated. The aqueous layer was extracted with CH Cl . The combined organics were washed with brine, dried over Na SO , filtered and concentrated in vacuo. The crude product was passed through a short silica gel pad eluting with 30% EtOAc/hexane to give 7- (difluoromethylsulfonyl)fluoro-indanone (18.8 g, 91%) as a white solid. LCMS ESI (+) m/z 265 (M+H).

Step F: Preparation of (1R)(difluoromethylsulfonyl)fluoro-indanol: A pear-shaped flask was charged with 7-(difluoromethylsulfonyl)fluoro-indanone (992 mg, 3.75 mmol), formic acid (0.178 mL, 4.69 mmol), triethylamine (0.576 mL, 4.13 mmol), and dichloromethane (25 mL). The reaction mixture was backfilled with nitrogen. RuCl(p- cymene)[(R,R)-Ts-DPEN] (48 mg, 0.08 mmol) was added in one portion, and the reaction mixture was stirred at ambient temperature overnight. The reaction was concentrated under reduced pressure. The residue was purified by flash chromatography on silica gel (5-20% EtOAc in hexanes) to give (1R)(difluoromethylsulfonyl)fluoro-indanol (990 mg, 99%) as a solid. The ee was determined to be 98% by F NMR analysis of the corresponding Mosher ester. LCMS ESI (+) m/z 267 (M+H); ESI (-) m/z 311 (M-H+46).

Step G: Preparation of (R)(3-chlorofluorophenoxy) ((difluoromethyl)sulfonyl)-2,3-dihydro-1H-indenol (Compound 1): A solution of 3- chlorofluoro-phenol (24 mg, 0.17 mmol) and (1R)(difluoromethylsulfonyl)fluoro- indanol (40 mg, 0.15 mmol) in NMP (1 mL) at ambient temperature was treated with NaHCO (37 mg, 0.45 mmol). The reaction mixture was stirred at 90 C under nitrogen for 4 hours. After cooling, the reaction mixture was partitioned between EtOAc and water. The aqueous layer was extracted with EtOAc. The combined organic layers were washed with water and brine, dried and concentrated. The residue was purified by C18 reverse phase flash chromatography (Biotage Isolera One unit, C18 Flash 12+M column, 10-60% CH CN/water) to give Compound 1 (25 mg, 42%). The ee was determined to be 98% by F NMR analysis of the corresponding Mosher ester. LCMS ESI (+) m/z 393 (M+H); ESI (-) m/z 437, 439 (M- H+46); H NMR (400 MHz, CDCl ): δ 7.81 (d, 1H), 7.00-6.89 (m, 3H), 6.73-6.71 (m, 1H), 6.35 (t, 1H), 5.66-5.65 (m, 1H), 3.19-3.13 (m, 2H), 2.96-2.90 (m, 1H), 2.50-2.40 (m, 1H), 2.30-2.24 (m, 1H).

Alternative synthesis of 4-fluorosulfanyl-indanone: Step A: A solution of (7-fluorooxo-indanyl) trifluoromethanesulfonate (237.0 mg, 0.79 mmol) and Xantphos (50.6 mg, 0.09 mmol) in 1,4-Dioxane (3 mL) was sparged with nitrogen for 3 mins. The reaction mixture was then treated sequentially with S- Potassium Thioacetate (136.1 mg, 1.19 mmol) and Tris(dibenzylideneacetone)dipalladium(0) (36.4 mg, 0.04 mmol) under continuous nitrogen stream. The vessel was sealed and heated to 100 C for 4 hours. The reaction mixture was filtered to remove insolubles with CH Cl used as a rinse. The filtrate was concentrated and purification was achieved by chromatography on silica using 10%-30% EtOAc/hexane to give S-(7-fluorooxo-indanyl) ethanethioate (99 mg, 0.44 mmol, 46% yield). LCMS ESI (+) m/z 225 (M+H).

Step B: To a round bottom flask containing S-(7-fluorooxo-indanyl) ethanethioate (99.0 mg, 0.4400 mmol) dissolved in 4.4 mL of degassed THF (sparged with nitrogen for 5 min) was added ammonium hydroxide (620 μL, 4.45 mmol). The resulting reaction mixture stirred for 40 minutes under nitrogen atmosphere. TLC indicates consumption of starting material and LCMS identifies the desired product. The reaction mixture was concentrated to remove excess THF and then poured into 1 mL of 1 M NaOH and 15 mL of water and rinsed with 2 x 20 mL of CH2Cl2. The remaining aqueous phase was acidified with 10 mL of 1 M HCl and extracted with 3 x 20 mL of CH Cl . The combined organic extracts were dried with MgSO , filtered, and concentrated to dryness. The product was used without further purification to give 4-fluorosulfanyl-indanone (44 mg, 0.24 mmol, 55% yield).

Example 2 (R)((Difluoromethyl)sulfonyl)(3,5-difluorophenoxy)-2,3-dihydro-1H- indenol (Compound 2): Prepared similarly as described in Example 1 using 3,5-difluoro- phenol in place of 3-chlorofluoro-phenol in Step G. LCMS ESI (+) m/z 377 (M+H); ESI (-) m/z 421 (M-H+46); H NMR (400 MHz, CDCl ): δ 7.81 (d, 1H), 6.96 (d, 1H), 6.73-6.68 (m, 1H), 6.62-6.61 (m, 2H), 6.36 (t, 1H), 5.66-5.65 (m, 1H), 3.22-3.10 (m, 2H), 2.96-2.90 (m, 1H), 2.50-2.40 (m, 1H), 2.29-2.24 (m, 1H).

Example 3 (R)((5-chloropyridinyl)oxy)((difluoromethyl)sulfonyl)-2,3-dihydro- 1H-indenol (Compound 3): Prepared similarly as described in Example 1 using 5- chloropyridinol in place of 3-chlorofluoro-phenol in Step G. LCMS ESI (+) m/z 376, 378 (M+H); H NMR (400 MHz, CDCl ): δ 8.49 (s, 1H), 8.36 (s, 1H), 7.81 (d, 1H), 7.44-7.43 (m, 1H), 6.89 (d, 1H), 6.36 (t, 1H), 5.67-5.66 (m, 1H), 3.23-3.16 (m, 2H), 2.99-2.92 (m, 1H), 2.51-2.42 (m, 1H), 2.32-2.25 (m, 1H).

Example 4 (R)((7-((Difluoromethyl)sulfonyl)hydroxy-2,3-dihydro-1H-inden yl)oxy)nicotinonitrile (Compound 4): Prepared similarly as described in Example 1 using 5- hydroxynicotinonitrile in place of 3-chlorofluoro-phenol in Step G. LCMS ESI (+) m/z 367 (M+H); H NMR (400 MHz, CDCl ): δ 8.76 (s, 1H), 8.66 (s, 1H), 7.86 (d, 1H), 7.65-7.64 (m, 1H), 6.93 (d, 1H), 6.38 (t, 1H), 5.71-5.65 (m, 1H), 3.20-3.16 (m, 2H), 2.96-2.90 (m, 1H), 2.50-2.42 (m, 1H), 2.37-2.24 (m, 1H).

Example 5 (R)((difluoromethyl)sulfonyl)((5-fluoropyridinyl)oxy)-2,3-dihydro- 1H-indenol (Compound 5): Prepared similarly as described in Example 1 using 5- fluoropyridinol in place of 3-chlorofluoro-phenol in Step G. LCMS ESI (+) m/z 360 (M+H); H NMR (400 MHz, CDCl ): δ 8.41 (s, 1H), 8.32 (s, 1H), 7.82 (d, 1H), 7.22-7.17 (m, 1H), 6.92 (d, 1H), 6.37 (t, 1H), 5.70-5.60 (m, 1H), 3.23-3.18 (m, 2H), 2.99-2.97 (m, 1H), 2.54-2.40 (m, 1H), 2.34-2.22 (m, 1H).

Example 6 (R)((difluoromethyl)sulfonyl)(3-fluoromethoxyphenoxy)-2,3- dihydro-1H-indenol (Compound 6): Prepared similarly as described in Example 1 using 3-fluoromethoxyphenol in place of 3-chlorofluoro-phenol in Step G. LCMS ESI (-) m/z 433 (M-H+46); H NMR (400 MHz, CDCl ): δ 7.77 (d, 1H), 6.91 (d, 1H), 6.54-6.50 (m, 1H), 6.42-6.38 (m, 2H), 6.39 (t, 1H), 5.67-5.63 (m, 1H), 3.80 (s, 3H), 3.23-3.15 (m, 2H), 2.99-2.92 (m, 1H), 2.50-2.45 (m, 1H), 2.30-2.23 (m, 1H).

Example 7 Step A: Preparation of 7-((difluoromethyl)sulfonyl)fluoromethyl-2,3- dihydro-1H-indenol: To a solution of 7-(difluoromethylsulfonyl)fluoromethyl-indan- 1-one (55 mg, 0.2 mmol, prepared similarly as described in Example 1 using 4-fluoro hydroxymethyl-2, 3-dihydro-1H-indenone in place of 4-fluorohydroxy-2,3-dihydro- 1H-indenone in Step A) in methanol (5 mL) at room temperature was added sodium borohydride (15 mg, 0.4 mmol) portion wise. The reaction was stirred at room temperature until starting material disappeared by TLC analysis. The reaction mixture was diluted with brine and extracted with EtOAc. The combined extract was dried over MgSO , filtered and concentrated. The crude product was used in the next step without further purification.

Step B: A mixture of 7-(difluoromethylsulfonyl)fluoromethyl-indanol (55 mg, 0.2 mmol, crude from step A), 3-chlorofluoro-phenol (57 mg, 0.39 mmol), and cesium bicarbonate (76 mg, 0.39 mmol) in 1-methylpyridone (2 mL) was heated under N at 90 C for 1 hour. LCMS indicated the presence of both product and starting material in the reaction mixture. The flask was resealed and heated at 100 C for 2 hours. The reaction mixture was cooled to room temperature, diluted with brine and extracted with EtOAc. The combined organic extracts were dried over MgSO , filtered and concentrated. Purification with preparative TLC with EtOAc/hexane (10%) followed by reverse phase column chromatography with water/acetonitrile (10% to 90%) gave racemic Compound 7a (2.4 mg, 3% from step A) and racemic Compound 7b (0.7 mg, 1% from step A). LCMS ESI (+) m/z 254 (M+H). Characterization for 7a: LCMS ESI (+) m/z 429, 431 (M+Na); H NMR (400 MHz, CDCl ): δ 7.81 (d, 1H), 7.01-6.98 (m, 1H), 6.91-6.89 (m, 2H), 6.75-6.71 (m, 1H), 6.34 (t, 1H), 5.58-5.53 (m, 1H), 3.48-3.40 (m, 1H), 3.22 (d, 1H), 2.66-2.59 (m, 1), 1.98-1.93 (m, 1H), 1.46 (d, 3H). Characterization for 7b: LCMS ESI (+) m/z 429, 431 (M+Na); H NMR (400 MHz, CDCl ): δ 7.81 (d, 1H), 7.01-6.97 (m, 1H), 6.92 (d, 1H), 6.89-6.88 (m, 1H), 6.73- 6.69 (m, 1H), 6.38 (t, 1H), 5.70-5.67 (m, 1H), 3.71-3.64 (m, 1H), 3.25 (d, 1H), 2.47-2.41 (m, 1H), 2.14-2.06 (m, 1H), 1.36 (d, 3H).

Example 8 Step A: Preparation of 7-((difluoromethyl)sulfonyl)fluoro-2,3- dihydrospiro[indene-1,2'-[1,3]dioxolane] (Compound 8): A mixture of 7- (difluoromethylsulfonyl)fluoro-indanone (114 mg, 0.43 mmol), ethylene glycol (4 mL, 0.43 mmol), p-toluenesulfonic acid monohydrate (4 mg, 0.02 mmol) and toluene (20 mL) was refluxed with azotropic removal of H O using a Dean-Stark trap. The reaction was monitored by LCMS and ethylene glycol was added twice (4 mL each time). After refluxing for about 6 hours, LCMS indicated about 50% conversion. The mixture was cooled to room temperature, diluted with saturated aqueous NaHCO , and extracted with EtOAc. The organic layer was dried over Na SO , filtered, and concentrated. The residue was purified by C18 reverse phase flash chromatography (Biotage Isolera One unit, 10-50% CH CN/water) to give incomplete separation of starting material and product. Fractions containing starting material and product were combined and used in the next step. LCMS ESI (+) m/z 309 (M+H).

Step B: Preparation of 4-(3-chlorofluorophenoxy) ((difluoromethyl)sulfonyl)-2,3-dihydrospiro[indene-1,2'-[1,3]dioxolane]. Prepared analogously to Step B of Example 7 using 7-((difluoromethyl)sulfonyl)fluoro-2,3- dihydrospiro[indene-1,2'-[1,3]dioxolane] in place of 7-((difluoromethyl)sulfonyl)fluoro methyl-2,3-dihydro-1H-indenol. LCMS ESI (+) m/z 435/437 (M+H).

Step C: Preparation of 4-(3-chlorofluoro-phenoxy) (difluoromethylsulfonyl)indanone: To a solution of 4-(3-chlorofluorophenoxy) ((difluoromethyl)sulfonyl)-2,3-dihydrospiro[indene-1,2'-[1,3]dioxolane] (5 mg, 0.012 mmol) in acetone (1 mL) at room temperature was added pyridinium p-toluenesulfonate (PPTS, 3 small crystals) and water (0.2 mL). The reaction was heated at 85 C in a sealed tube for 1 hour. LCMS indicated a clean reaction with about 1:1 mixture of product: starting material.

Additional 4-(3-chlorofluorophenoxy)((difluoromethyl)sulfonyl)-2,3- dihydrospiro[indene-1,2'-[1,3]dioxolane] (45 mg) in acetone (3 mL) was added, followed by PPTS (20 mg, 0.08 mmol) and water (0.3 mL). The reaction mixture was heated at 90 C for 4 hours, concentrated, and purified by C18 reverse phase flash chromatography (Biotage Isolera One unit, 10-90% CH CN/water) to give 4-(3-chlorofluoro-phenoxy) (difluoromethylsulfonyl)indanone (42 mg, 0.11 mmol, 94% yield). LCMS ESI (+) m/z 391/393 (M+H).

Step D: Preparation of (E, Z)-N-butyl(3-chlorofluorophenoxy) ((difluoromethyl)sulfonyl)-2,3-dihydro-1H-indenimine: A mixture of 4-(3-chloro fluoro-phenoxy)(difluoromethylsulfonyl)indanone (42 mg, 0.11 mmol), 4 Å molecule sieves (300 mg, 0.11 mmol), trifluoroacetic acid (5 drops) and butanamine (840 mg, 11.5 mmol) in benzene (1.2 mL) was heated under nitrogen in a sealed tube at 80 C for 2 hours.

The reaction was not complete by HNMR analysis. The reaction mixture was transferred to a round bottom flask. Additional benzene (20 mL) and butaneamine (0.5 mL) were added.

The reaction mixture was refluxed with azeotropic removal of water using a Dean-Stark trap.

After one hour, additional benzene (10 mL) and butaneamine (0.5 mL) were added. The procedure was repeated one more time. After refluxing for two additional hours, the reaction mixture was concentrated and then dissolved in t-butyl ethyl ether. The organic layer was washed with saturated aqueous NaHCO and then brine, dried over Na SO , filtered, and 3 2 4 concentrated. The crude imine (E, Z)-N-butyl(3-chlorofluorophenoxy) ((difluoromethyl)sulfonyl)-2,3-dihydro-1H-indenimine was used in the next step without further purification.

Step E: Preparation of 4-(3-chlorofluoro-phenoxy) (difluoromethylsulfonyl)-2,2-difluoro-indanone: A mixture of (E, Z)-N-butyl(3-chloro- -fluoro-phenoxy)(difluoromethylsulfonyl)indanimine (48 mg, 0.11 mmol, crude from Step D), sodium sulfate (200 mg, 0.11 mmol) and Selectfluor (95 mg, 0.27 mmol) in anhydrous acetonitrile (10 mL) was heated at 85 C under N for 4 hours. After the reaction mixture was cooled to room temperature, HCl (37%, 1 mL) was added. The reaction mixture was stirred at room temperature for 15 minutes, and concentrated. The residue was diluted with EtOAc, washed with saturated NaHCO and brine, dried over Na SO , filtered, and 3 2 4 concentrated. The crude product was used in the next step without further purification. LCMS ESI (+) m/z 444/446 (M+NH4).

Step F: Preparation of 4-(3-chlorofluoro-phenoxy) (difluoromethylsulfonyl)-2,2-difluoro-indanol (Compound 8): To a solution of 4-(3- chlorofluoro-phenoxy)(difluoromethylsulfonyl)-2,2-difluoro-indanone (crude from Step E) in methanol (4 mL) was added sodium borohydride (100 mg, 2.64 mmol). The reaction was stirred at room temperature for 20 minutes. The reaction mixture was poured into brine, extracted with EtOAc, dried over MgSO , filtered, and concentrated. The residue was purified twice by preparative TLC with EtOAc/hexane (15%) to give Compound 8 (14 mg, 30% from Step E). LCMS ESI (+) m/z 429, 431 (M+H). H NMR (400 MHz, CDCl ): δ 7.90 (d, 1H), 7.06-7.03 (m, 1H), 6.98 (d, 1H), 6.94-6.92 (m, 1H), 6.78-6.74 (m, 1H), 6.42 (t, 1H), 5.50 (d, 1H), 3.61-3.43 (m, 2H), 3.24 (s, 1H).

Example 9 7-(difluoromethylsulfonyl)(3,5-difluorophenoxy)-2,2-difluoro-indanol (Compound 9): Prepared analogously to the procedure for Compound 8 in Example 8.

LCMS ESI (+) m/z 413 (M+H); H NMR (400 MHz, CDCl ): δ 7.90 (d, 1H), 7.01 (d, 1H), 6.80-6.73 (m, 1H), 6.70-6.63 (m, 2H), 6.43 (t, 1H), 5.50 (m, 1H), 3.60-3.43 (m, 2H), 3.30 (d, 1H).

Example 10 7-(3-chlorofluoro-phenoxy)(difluoromethylsulfonyl)indanol (Compound 10) Step A: Preparation of 4-bromo(3-chlorofluoro-phenoxy)indanone: A mixture of 4-bromofluoro-indanone (50 mg, 0.22 mmol), 3-chlorofluoro-phenol (48 mg, 0.33 mmol) and cesium bicarbonate (50.8 mg, 0.26 mmol) in 1-methylpyrrolidone (1.5 mL) was heated at 100 C for 2 hours. LCMS indicated about 40% conversion. The reaction mixture was heated for another 2 hours at 110 C and directly purified by C18 reverse phase flash chromatography (Biotage Isolera One unit, 10-80% CH CN/water) to give 4-bromo(3-chlorofluoro-phenoxy)indanone (27 mg, 0.08 mmol, 35% yield).

LCMS ESI (+) m/z 355, 357, 359 (M+H).

Step B: Preparation of S-[7-(3-chlorofluoro-phenoxy)oxo-indanyl] ethanethioate: A mixture of 4-bromo(3-chlorofluoro-phenoxy)indanone (22 mg, 0.06 mmol), Pd2(dba)3 (2.8 mg), xantphos (3.58 mg, 0.01 mmol) and S-potassium thioacetate (17.7 mg, 0.15 mmol) was heated in a microwave at 150 C under N for 30 minutes. The reaction mixture was concentrated under reduced pressure and purified by flash chromatography with EtOAc/hexane (0% to 30%) to give S-[7-(3-chlorofluoro-phenoxy)- 1-oxo-indanyl] ethanethioate (8.3 mg, 0.02 mmol, 38% yield). LCMS ESI (+) m/z 351, 353 (M+H).

Step C: Preparation of 7-(3-chlorofluoro-phenoxy)sulfanyl-indanone: To a solution of S-[7-(3-chlorofluoro-phenoxy)oxo-indanyl] ethanethioate (8.3 mg, 0.02 mmol) in tetrahydrofuran (6 mL) at room temperature under nitrogen was added ammonium hydroxide (0.2 mL). The reaction mixture was stirred at room temperature for 1.5 hours and then concentrated. The residue was dissolved in EtOAc and washed with 1 N HCl, dried over MgSO , filtered, and concentrated. The crude product was used in the next step without further purification. LCMS ESI (-) m/z 307, 309 (M-H).

Step D: Preparation of 7-(3-chlorofluoro-phenoxy) (difluoromethylsulfanyl)indanone: To a mixture of KOH (13.27 mg, 0.24 mmol) and 7-(3- chlorofluoro-phenoxy)sulfanyl-indanone (7.3 mg, 0.02 mmol) in a mixture of water (0.4 mL) and acetonitrile (1.5 mL) at -5 C was added bromodifluoromethyl diethylphosphonate (0.01 mL, 0.07 mmol). The reaction mixture was stirred at room temperature for 3 hours, diluted with brine, and extracted with EtOAc. The organic layer was dried over MgSO , filtered, and concentrated. The residue was purified by flash column chromatography with EtOAc/hexane (0% to 40%) to give 7-(3-chlorofluoro-phenoxy) (difluoromethylsulfanyl)indanone (3.5 mg, 0.01 mmol, 41% yield). LCMS ESI (+) m/z 359, 361 (M+H).

Step E: Preparation of 7-(3-chlorofluoro-phenoxy) (difluoromethylsulfonyl)indanone: A mixture of 7-(3-chlorofluoro-phenoxy) (difluoromethylsulfanyl)indanone (3.5 mg, 0.01 mmol), ruthenium trichloride (0.1 mg), and sodium periodate (6.3 mg, 0.03 mmol) in a mixture of acetonitrile (1 mL), carbon tetrachloride (1 mL), and water (2 mL) was stirred at room temperature for 3 hours. The reaction mixture was diluted with brine, extracted with EtOAc. The organic layer was dried over MgSO , filtered, and concentrated. The residue was purified by flash column chromatography with EtOAc/hexane (0% to 60%) to give 7-(3-chlorofluoro-phenoxy) (difluoromethylsulfanyl)indanone (3.5 mg, 0.01 mmol, quant.). LCMS ESI (+) m/z 391, 393 (M+H).

Step F: Preparation of 7-(3-chlorofluoro-phenoxy) (difluoromethylsulfonyl)indanol (Compound 10): To a solution of 7-(3-chlorofluoro- phenoxy)(difluoromethylsulfonyl)indanone (4 mg, 0.01 mmol) in methanol (1 mL) at room temperature was added sodium borohydride (10 mg, 0.26 mmol) portion wise. The reaction mixture was stirred at room temperature for 30 minutes and directly purified by preparative TLC with EtOAc/hexane (35%) to give Compound 10 (2.8 mg, 0.007 mmol, 70% yield). LCMS ESI (+) m/z 375, 377 (M-OH). H NMR (400 MHz, CDCl ): δ 7.85 (d, 1H), 7.04-7.00 (m, 1H), 6.97-6.95 (m, 1H), 6.84-6.77 (m, 2H), 6.18 (t, 1H), 5.58-5.53 (m, 1H), 3.59-3.50 (m, 1H), 3.34-3.26 (m, 1H), 2.60-2.50 (m, 1H), 2.31 (d, 1H), 2.21-2.13(m, 1H).

Example 11 3-[7-(difluoromethylsulfonyl)-2,2-difluorohydroxy-indanyl]oxy fluoro-benzonitrile (Compound 11): Prepared analogously to the procedure for Compound 8. LCMS ESI (+) m/z 437 (M+NH ); H NMR (400 MHz, CDCl ): δ 7.94 (d, 1H), 7.33-7.29 (m, 1H), 7.23-7.21 (m, 1H), 7.13-7.09 (m, 1H), 7.00 (d, 1H), 6.43 (t, 1H), 5.51 (d, 1H), 3.60- 3.43 (m, 2H), 3.30 (br s, 1H).

Example 12 1-allyl(difluoromethylsulfonyl)(3,5-difluorophenoxy)-2,2-difluoro- indanol (Compound 12): A mixture of 7-(difluoromethylsulfonyl)(3,5- difluorophenoxy)-2,2-difluoro-indanone (prepared analogously to the procedures in Example 8, 24 mg, 0.06 mmol), 3-iodopropene (0.05 mL, 0.58 mmol), and indium (67 mg, 0.58 mmol) in N,N-dimethylformamide (2 mL) was stirred at room temperature overnight.

The reaction mixture was diluted with 1:1 water/brine and extracted with EtOAc. The organic layer was dried over MgSO , filtered, and concentrated. The residue was purified by flash column chromatography with EtOAc/hexane (30%) to give Compound 12 (9.7 mg, 0.02 mmol, 37% yield). LCMS ESI (-) m/z 451 (M-H); H NMR (400 MHz, CDCl ): δ 8.01 (d, 1H), 6.97 (d, 1H), 6.82-6.55 (m, 4H), 5.76-5.64 (m, 1H), 5.35-5.26 (m, 2H), 3.54-3.44 (m, 2H), 3.31-3.18 (m, 1H), 3.06-2.96 (m, 2H).

Example 13 3-[7-(difluoromethylsulfonyl)-2,2-difluorohydroxymethyl-indan yl]oxyfluoro-benzonitrile (Compound 13): To a solution of 3-[7- (difluoromethylsulfonyl)-2,2-difluorooxo-indanyl]oxyfluoro-benzonitrile (4.8 mg, 0.01 mmol) in tetrahydrofuran (4 mL) at room temperature was added dimethylzinc (0.01 mL, 0.01 mmol). The reaction was heated to 80 C for 1 hour. The reaction mixture was directly purified by preparative TLC with EtOAc/hexane (30%) to give Compound 13 (2.1 mg, 0.005 mmol, 42% yield). LCMS ESI (+) m/z 451 (M+NH ); H NMR (400 MHz, CDCl ): δ 8.0 (d, 1H), 7.33-7.30 (m, 1H), 7.23-7.21 (m, 1H), 7.13-7.09 (m, 1H), 6.92 (d, 1H), 6.62 (m, 1H), 3.58-3.49 (m, 2H), 3.34-3.20 (m, 1H), 1.84-1.82 (m, 3H).

Example 14 2-[7-(3,5-difluorophenoxy)hydroxy-indanyl]sulfonylacetonitrile (Compound 14) Step A: Preparation of 2-(7-fluorooxo-indanyl)sulfanylacetonitrile: A mixture of 4-fluorosulfanyl-indanone (prepared from 1 g of S-(7-fluorooxo-indan yl)-N,N-dimethylcarbamothioate according to Step C of Example 1), sodium carbonate (1 g, 9.43 mmol) and bromoacetonitrile (719.7 mg, 6 mmol) was heated at 60 C overnight. The reaction mixture was concentrated under reduced pressure. The residue was purified by flash column chromatography with EtOAc/hexane (0% to 30%) to give 980 mg of 2-(7-fluoro oxo-indanyl)sulfanylacetonitrile as a brown solid (quant. yield).

Steps B-F: 2-[7-(3,5-Difluorophenoxy)hydroxy-indan yl]sulfonylacetonitrile (Compound 14) was prepared analogously to the procedures in Example 1. LCMS ESI (-) m/z 364 (M-H); H NMR (400 MHz, CDCl ): δ 7.9 (d, 1H), 6.97 (d, 1H), 6.73-6.67 (m 1H), 6.64-6.58 (m, 1H), 5.83-5.79 (m, 1H), 6.57-6.53 (m, 1H), 4.22 (d, 1H), 3.20-3.10 (m, 1H), 2.95-2.85 (m, 2H), 2.60-2.50 (m, 1H), 2.25-2.16 (m, 1H).

Example 15 3-[(1S)(difluoromethylsulfonyl)-2,2-difluorohydroxy-indanyl]oxy fluoro-benzonitrile (Compound 15) Step A: Preparation of 3-((7-((difluoromethyl)sulfonyl)-2,3- dihydrospiro[indene-1,2'-[1,3]dioxolan]yl)oxy)fluorobenzonitrile: A mixture of 3- fluorohydroxy-benzonitrile (1.33 g, 9.7 mmol), 7'-(difluoromethylsulfonyl)-4'-fluoro- spiro[1,3-dioxolane-2,1'-indane] (1.0 g, 3.24 mmol), and cesium bicarbonate (1.26 g, 6.5 mmol) in 1-methylpyrrolidone (1.8 mL) was heated under N at 110 C (microwave) for 1 hour and 5 minutes. The reaction was repeated ten times. The reaction mixtures were combined, diluted with EtOAc, and washed twice with 1 N NaOH. The combined aqueous layer was extracted with EtOAc. The EtOAc extracts were combined and washed with brine, dried over Na SO , filtered, and concentrated to about 100 mL to give a suspension. The suspension was filtered to give 3-((7-((difluoromethyl)sulfonyl)-2,3-dihydrospiro[indene- 1,2'-[1,3]dioxolan]yl)oxy)fluorobenzonitrile as an off-white solid (6.25 g). The filtrate was diluted with EtOAc, washed with brine (3X), dried over Na SO , filtered, and concentrated. The residue was purified by flash column chromatography on silica gel with EtOAc/hexane (0% to 40%) to give additional 3-((7-((difluoromethyl)sulfonyl)-2,2-difluoro- 2,3-dihydrospiro[indene-1,2'-[1,3]dioxolan]yl)oxy)fluorobenzonitrile (3.3 g, 69% combined yield) as a white solid. LCMS ESI (+) m/z 426 (M+H).

Step B: Preparation of 3-((7-((difluoromethyl)sulfonyl)oxo-2,3-dihydro- 1H-indenyl)oxy)fluorobenzonitrile: A mixture of 3-((7-((difluoromethyl)sulfonyl)-2,3- dihydrospiro[indene-1,2'-[1,3]dioxolan]yl)oxy)fluorobenzonitrile (10.9 g, 25.6 mmol) and PPTS (667 mg, 2.66 mmol) in acetone (100 mL)/water (15 mL) was heated at 82 C for 5 hours and then 75 C overight. The reaction mixture was cooled to room temperature, concentrated under reduced pressure, diluted with EtOAc, washed with saturated aqueous NaHCO , dried over MgSO , filtered, and concentrated. The residue was filtered and washed with water. The solid obtained was briefly dried under vacuum at 50 C and then triturated with EtOAc/hexane to give 3-((7-((difluoromethyl)sulfonyl)oxo-2,3-dihydro-1H-inden yl)oxy)fluorobenzonitrile (8 g). Flash column chromatography of the mother liquor on silica gel with EtOAc/hexane (0% to 80%) provided additional 3-((7- ((difluoromethyl)sulfonyl)oxo-2,3-dihydro-1H-indenyl)oxy)fluorobenzonitrile (1.3 g, combined 9.3 g, quant. yield). LCMS ESI (+) m/z 382 (M+H).

Step C: Preparation of (E, Z)((1-(butylimino)((difluoromethyl)sulfonyl)- 2,3-dihydro-1H-indenyl)oxy)fluorobenzonitrile: A mixture of 3-((7- ((difluoromethyl)sulfonyl)oxo-2,3-dihydro-1H-indenyl)oxy)fluorobenzonitrile (1.42 g, 3.72 mmol), butylamine (6.0 mL) and 5 drops of trifluoroacetic acid (~ 0.1 mL) in benzene (40 mL) was refluxed overnight with removal of water using a Dean-Stark trap. The reaction mixture was concentrated under reduced pressure, diluted with methyl tert-butyl ether, washed with saturated aqueous NaHCO3 and brine, dried over Na2SO4, filtered, and concentrated. The residue was used in the next step without further purification.

Step D: Preparation of 3-((7-((difluoromethyl)sulfonyl)-2,2-difluorooxo- 2,3-dihydro-1H-indenyl)oxy)fluorobenzonitrile: A mixture of (E, Z)((1-(butylimino)- 7-((difluoromethyl)sulfonyl)-2,3-dihydro-1H-indenyl)oxy)fluorobenzonitrile (1.29 g, 3 mmol, crude from step C), Selectfluor (2.62 g, 7.4 mmol) and sodium sulfate (4 g, 28.2 mmol) under N was heated at 82 C for 4 hours. After cooling to room temperature, concentrated HCl (37%, 3 mL) was added. The mixture was stirred at room temperature for minutes and then concentrated under reduced pressure. The residue was diluted with methyl t-butyl ether, washed with half saturated aqueous NaHCO and then brine, dried over Na SO , filtered, and triturated with EtOAc/hexane to give 3-((7-((difluoromethyl)sulfonyl)- 2,2-difluorooxo-2,3-dihydro-1H-indenyl)oxy)fluorobenzonitrile as an off-white solid (0.5 g). The mother liquor was purified by flash column chromatography with EtOAc/hexane (5% to 40%) to give additional 3-((7-((difluoromethyl)sulfonyl)-2,2-difluorooxo-2,3- dihydro-1H-indenyl)oxy)fluorobenzonitrile (0.13 g, 51% combined yield). LCMS ESI (+) m/z 418 (M+H) and 435 (M+NH ).

Step E: Preparation of (S)((7-((difluoromethyl)sulfonyl)-2,2-difluoro hydroxy-2,3-dihydro-1H-indenyl)oxy)fluorobenzonitrile (Compound 15): An ice cold solution of RuCl(p-cymene)[(R,R)-Ts-DPEN] (0.6 mg) in dichloromethane (0.2 mL) was added by syringe under nitrogen to an ice cold solution of 3-[7-(difluoromethylsulfonyl)-2,2- difluorooxo-indanyl]oxyfluoro-benzonitrile (28 mg, 0.07 mmol), triethylamine (18.7 μL, 0.13 mmol) and formic acid (7.6 μL, 0.2 mmol) in dichloromethane (0.5 mL) and then placed in a refrigerator at 4 C overnight. The reaction mixture was directly purified on preparative TLC with EtOAc/hexane (40%) to give Compound 15 (23.4 mg, 0.06 mmol, 83% yield). The ee was determined to be greater than 95% by F NMR analysis of the corresponding Mosher ester. LCMS ESI (+) m/z 420 (M+H); H NMR (400 MHz, CDCl ): δ 7.94 (d, 1H), 7.33-6.98 (m, 4H), 6.44 (t, 1H), 5.51 (d, 1H), 3.61-3.45 (m, 2H).

Example 16 (S)(3-chlorofluorophenoxy)((difluoromethyl)sulfonyl)-2,3-dihydro- 1H-indenol (Compound 16): Prepared similarly as described in Example 1 using RuCl(p- cymene)[(S,S)-Ts-DPEN] in place of RuCl(p-cymene)[(R,R)-Ts-DPEN] in Step F. The e.e. was determined to be 96% by F NMR analysis of the corresponding Mosher ester. LCMS ESI (+) m/z 393 (M+H); ESI (-) m/z 437/439 (M-H+46); H NMR (400 MHz, CDCl ): δ 7.81 (d, 1H), 7.00-6.98 (m, 1H), 6.94 (d, 1H), 6.89-6.88 (m, 1H), 6.74-6.71 (m, 1H), 6.35 (t, 1H), .67-5.65 (m, 1H), 3.21-3.13 (m, 2H), 2.96-2.89 (m, 1H), 2.50-2.41 (m, 1H), 2.30-2.23 (m, 1H).

Example 17 4-(3-chlorofluorophenoxy)((difluoromethyl)sulfonyl)-2,3-dihydro-1H- indenol (Compound 17) Step A: Preparation of 7-(difluoromethylsulfonyl)fluoro-indanol: To a stirred solution of 7-(difluoromethylsulfonyl)fluoro-indanone (110 mg, 0.42 mmol) in methanol (4 mL) was added sodium borohydride (24 mg, 0.62 mmol). The reaction mixture was stirred at ambient temperature for 1 hour. Saturated aqueous NH Cl solution was added dropwise. The mixture was extracted with EtOAc. The combined organic layers were washed with water and brine, dried and concentrated in vacuo to give 7-(difluoromethylsulfonyl) fluoro-indanol (100 mg, 90%), which was used in the next step without further purification. LCMS ESI (+) m/z 267 (M+H); ESI (-) m/z 311 (M-H+46).

Step B: Preparation of 4-(3-chlorofluorophenoxy) ((difluoromethyl)sulfonyl)-2,3-dihydro-1H-indenol (Compound 17): Prepared similarly as described in Example 1 Step G using 7-(difluoromethylsulfonyl)fluoro-indanol in place of (1R)(difluoromethylsulfonyl)fluoro-indanol. LCMS ESI (+) m/z 393 (M+H); ESI (-) m/z 437, 439 (M-H+46).

Example 18 4-(3-chlorofluorophenoxy)((difluoromethyl)sulfonyl)-2,3-dihydro-1H- indenone (Compound 18): To a stirred solution of 4-(3-chlorofluoro-phenoxy) (difluoromethylsulfonyl)indanol Compound 17 (23 mg, 0.06 mmol) in dichloromethane (1 mL) was added Dess-Martin periodinane (37 mg, 0.09 mmol). The reaction mixture was stirred at ambient temperature for 3 hours. The reaction mixture was partitioned between EtOAc and water. The aqueous layer was extracted with EtOAc. The combined organic layers were washed with water and brine, dried and concentrated. The residue was purified by flash chromatography on silica gel (5-20% EtOAc in hexane) to give Compound 18 (20 mg, 87%) as a white solid. LCMS ESI (+) m/z 391, 393 (M+H); H NMR (400 MHz, CDCl ): δ 8.15 (d, 1H), 7.14 (d, 1H), 7.12 (t, 1H), 7.07-7.04 (m, 1H), 6.96-6.93 (m, 1H), 6.80-6.76 (m, 1H), 3.23-3.20 (m, 2H), 2.90-2.87 (m, 2H).

Example 19 7-((difluoromethyl)sulfonyl)(3,5-difluorophenoxy)-2,3-dihydro-1H-inden- 1-amine (Compound 19) Step A: Preparation of 7-((difluoromethyl)sulfonyl)(3,5-difluorophenoxy)- 2,3-dihydro-1H-indenone: Prepared as described in Example 18 using (R) ((difluoromethyl)sulfonyl)(3,5-difluorophenoxy)-2,3-dihydro-1H-indenol (Compound 2) in place of 4-(3-chlorofluoro-phenoxy)(difluoromethylsulfonyl)indanol (Compound 17). LCMS ESI (+) m/z 375 (M+H).

Step B: Preparation of 7-((difluoromethyl)sulfonyl)(3,5-difluorophenoxy)- 2,3-dihydro-1H-indenamine (Compound 19): A mixture of 7-((difluoromethyl)sulfonyl)- 4-(3,5-difluorophenoxy)-2,3-dihydro-1H-indenone (25 mg, 0.07 mmol) and NH OAc (51 mg, 0.67 mmol) in i-PrOH (0.77 mL) was stirred at ambient temperature for 1 hour.

NaBH CN (17 mg, 0.27 mmol) was added. The mixture was heated at reflux for 1 hour. After cooling, the reaction was quenched by the addition of saturated aqueous NaHCO solution.

The aqueous layer was extracted with dichloromethane. The combined organic layers were washed with brine, dried and concentrated. The residue was purified by flash chromatography on silica gel (2-12% MeOH in dichloromethane) to give Compound 19, which was converted to HCl salt by treatment with 4N HCl in dioxane (4 mg, 16% yield). LCMS ESI (+) m/z 376 (M+H). H NMR for free base (400 MHz, CDCl ): δ 7.81 (d, 1H), 6.92 (d, 1H), 6.72-6.67 (m, 1H), 6.62 (t, 1H), 6.63-6.59 (m, 2H), 4.96-4.94 (m, 1H), 3.18-3.10 (m, 1H), 2.99-2.92 (m, 1H), 2.51-2.41 (m, 1H), 2.30-2.00 (m, 3H).

Example 20 4-((Difluoromethyl)sulfonyl)(3,5-difluorophenoxy)-2,3-dihydro-1H-indene (Compound 20): To a mixture of ((1R)(difluoromethylsulfonyl)(3,5- difluorophenoxy)indanol (Compound 2) (25 mg, 0.07 mmol), triethylsilane (0.13 mL, 0.80 mmol), and EtOH (0.7 mL) was added Pd(OH) /C (20% load on carbon, 5 mg). The reaction mixture was heated at reflux overnight. After cooling, the reaction mixture was filtered through Celite. The filtrate was concentrated. The residue was purified by C18 reverse phase flash chromatography (Biotage Isolera One unit, C18 Flash 12+M column, 30- 95% CH CN/water) to afford Compound 20 (10 mg, 42%) as a white solid. LCMS ESI (+) m/z 361 (M+H); H NMR (400 MHz, CDCl ): δ 7.76 (d, 1H), 6.87 (d, 1H), 6.69-6.63 (m, 1H), 6.60-6.55 (m, 2H), 6.18 (t, 1H), 3.37 (t, 2H), 2.93 (t, 2H), 2.20-2.17 (m, 2H).

Example 21 4-((Difluoromethyl)sulfonyl)(3,5-difluorophenoxy)-1H-indene (Compound 21): A mixture of 7-(difluoromethylsulfonyl)(3,5-difluorophenoxy)indan ol (60 mg, 0.16 mmol), p-toluenesulfonic acid monohydrate (9.1 mg, 0.05 mmol) and toluene (1.6 mL) was heated at 100 C for 5 hours. After cooling, the reaction mixture was concentrated. The residue was purified by C18 reverse phase flash chromatography (Biotage Isolera One unit, C18 Flash 12+M column, 20-60% CH CN/water) to afford Compound 21 (50 mg, 88% yield) as a solid. LCMS ESI (+) m/z 359 (M+H); H NMR (400 MHz, CDCl ): δ 7.88 (d, 1H), 7.47-7.45 (m, 1H), 6.93-6.90 (m, 2H), 6.71-6.60 (m, 3H), 6.22 (t, 1H), 3.49- 3.48 (m, 1H).

Example 22 4-((Difluoromethyl)sulfonyl)(3,5-difluorophenoxy)-2,3-dihydro-1H-inden- 2-ol (Compound 22) Step A: Preparation of 2-((difluoromethyl)sulfonyl)(3,5-difluorophenoxy)- 1a,6a-dihydro-6H-indeno[1,2-b]oxirene: To a stirred solution of 4-(difluoromethylsulfonyl)- 7-(3,5-difluorophenoxy)-1H-indene (Compound 21) (30 mg, 0.08 mmol) in dichloromethane (0.4 mL) was added 3-chloroperbenzoic acid (38 mg, 0.17 mmol). The reaction mixture was stirred for 40 hours at ambient temperature. The reaction mixture then diluted with dichloromethane, washed with 20% sodium carbonate, dried over anhydrous sodium sulfate and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel (15% EtOAc in hexane) to afford 2-((difluoromethyl)sulfonyl)- -(3,5-difluorophenoxy)-1a,6a-dihydro-6H-indeno[1,2-b]oxirene (24 mg, 77%). LCMS ESI (-) m/z 357 (M-H-16).

Step B: Preparation of 4-((difluoromethyl)sulfonyl)(3,5-difluorophenoxy)- 2,3-dihydro-1H-indenol (Compound 22): To a stirred solution of 2- ((difluoromethyl)sulfonyl)(3,5-difluorophenoxy)-1a,6a-dihydro-6H-indeno[1,2-b]oxirene (24 mg, 0.06 mmol) in 1,2-dichloroethane (0.6 mL) was added diiodozinc (31 mg, 0.1 mmol) and sodium cyanoborohydride (8.1 mg, 0.13 mmol). The reaction mixture was heated to reflux for 16 hours. After cooling, the reaction was quenched by the addition of 1N HCl. The mixture was extracted with dichloromethane. The combined organic layers were washed with brine, dried and concentrated. The residue was purified by flash chromatography on silica gel (10-30% EtOAc in hexane) to give Compound 22 (7 mg, 29%). LCMS ESI (-) m/z 421 (M- H+46); H NMR (400 MHz, CDCl ): δ 7.79 (d, 1H), 6.90 (d, 1H), 6.72-6.66 (m, 1H), 6.64- 6.57 (m, 2H), 6.19 (t, 1H), 4.85-4.81 (m, 1H), 3.60-3.44 (m, 3H), 3.21-2.99 (m, 2H).

Example 23 cis-(±)7-((Difluoromethyl)sulfonyl)(3,5-difluorophenoxy)-2,3-dihydro-1H- indene-1,2-diol (Compound 23): Two diols were isolated as a mixture of two diastereomers from Example 22 Step B by further elution of the silica gel column with 50% EtOAc in hexane. The mixture was further purified by C18 reverse phase flash chromatography (Biotage Isolera One unit, C18 Flash 12+M column, 20-50% CH CN/water) to give Compound 23 (4 mg, 16%) as a solid. LCMS ESI (-) m/z 437 (M-H+46); H NMR (400 MHz, CDCl ): δ 7.83 (d, 1H), 6.98 (d, 1H), 6.74-6.69 (m, 1H), 6.64-6.62 (m, 2H), 6.36 (t, 1H), 5.37 (brs, 1H), 4.65-4.63 (m, 1H), 3.45-3.39 (m, 2H), 2.92-2.88 (m, 1H).

Example 24 (7-((Difluoromethyl)sulfonyl)(3,5-difluorophenoxy)-2,3-dihydro-1H-inden- 1-yl)methanol (Compound 24) Step A: Preparation of 7-((difluoromethyl)thio)fluoro-2,3-dihydro-1H- indenecarbaldehyde: Lithium bis(trimethylsilyl)amide (1.0 M solution in THF, 0.32 mL, 0.32 mmol) was added dropwise to a stirred suspension of (methoxy methyl)triphenylphosphonium chloride (103 mg, 0.30 mmol) in dry THF (1 mL) at 0 °C under nitrogen. The mixture was stirred at 0 °C for 1 hour. A solution of 7- (difluoromethylsulfanyl)fluoro-indanone (50 mg, 0.22 mmol) in THF (1 mL) was added dropwise. The mixture was stirred at 0 °C for 1 hour and at ambient temperature overnight.

Water was added and the mixture was partitioned between EtOAc and brine. The aqueous layer was extracted with EtOAc. The combined organic layers were washed with brine, dried and concentrated. The crude was dissolved in tetrahydrofuran (2 mL). Concentrated HCl (0.11 mL) was added. The reaction mixture was stirred at ambient temperature for 4 hours, and then extracted with EtOAc. The combined organic layers were washed with brine, dried and concentrated. The residue was purified by flash chromatography on silica gel (10-50% EtOAc/hexane) to give 7-((difluoromethyl)thio)fluoro-2,3-dihydro-1H-indene carbaldehyde (24 mg, 45%). LCMS ESI (-) m/z 245 (M-H).

Step B: Preparation of (7-((difluoromethyl)thio)fluoro-2,3-dihydro-1H- indenyl)methanol: To a stirred solution of 7-((difluoromethyl)thio)fluoro-2,3-dihydro- 1H-indenecarbaldehyde (24 mg, 0.10 mmol) in MeOH (1 mL) was added sodium borohydride (5.5 mg, 0.15 mmol). The reaction mixture was stirred at ambient temperature for 30 minutes. Water was added dropwise to quench the reaction. The mixture was extracted with EtOAc. The combined organic layers were washed with water and brine, dried and concentrated. The residue was purified by flash chromatography on silica gel (10-50% EtOAc/hexane) to give (7-((difluoromethyl)thio)fluoro-2,3-dihydro-1H-inden yl)methanol (17 mg, 70% yield). LCMS ESI (-) m/z 247 (M-H).

Step C: Preparation of (7-((difluoromethyl)sulfonyl)fluoro-2,3-dihydro-1H- indenyl)methanol: To a stirred solution of (7-((difluoromethyl)thio)fluoro-2,3-dihydro- 1H-indenyl)methanol (17 mg, 0.07 mmol) in dichloromethane (0.7 mL) was added 3- chloroperbenzoic acid (35 mg, 0.21 mmol). The reaction mixture was stirred at ambient temperature overnight. The reaction was quenched by the addition of saturated aqueous NaHCO solution and saturated aqueous Na S O solution and then extracted twice with 3 2 2 3 EtOAc. The combined organic layers were washed with water and brine, dried and concentrated. The residue was purified by flash chromatography on silica gel (10-30% EtOAc/hexane) to give (7-((difluoromethyl)sulfonyl)fluoro-2,3-dihydro-1H-inden yl)methanol (14 mg, 73%). LCMS ESI (+) m/z 281 (M+H).

Step D: Preparation of (7-((difluoromethyl)sulfonyl)(3,5-difluorophenoxy)- 2,3-dihydro-1H-indenyl)methanol (Compound 24): Prepared similarly as described in Example 1 Step G using (7-((difluoromethyl)sulfonyl)fluoro-2,3-dihydro-1H-inden yl)methanol in place of (1R)(difluoromethylsulfonyl)fluoro-indanol. LCMS ESI (+) 391 m/z (M+H); H NMR (400 MHz, CDCl ): δ 7.77 (d, 1H), 6.90 (d, 1H), 6.71-6.65 (m, 1H), 6.62-6.36 (m, 2H), 6.23 (t, 1H), 3.94-3.71 (m, 3H), 2.97-2.89 (m, 2H), 2.84 (s, 1H), 2.40-2.22 (m, 2H).

Example 25 (S)((5-chloropyridinyl)oxy)((difluoromethyl)sulfonyl)-2,2-difluoro- 2,3-dihydro-1H-indenol (Compound 25) Step A: Preparation of 3-chloro((7-((difluoromethyl)sulfonyl)-2,3- dihydrospiro[indene-1,2'-[1,3]dioxolan]yl)oxy)pyridine: 7-((Difluoromethyl)sulfonyl) fluoro-2,3-dihydrospiro[indene-1,2'-[1,3]dioxolane] (3.0 g, 9.7 mmol) was combined with 5- chloropyridinol (1.89 g, 14.6 mmol) and sodium bicarbonate (2.45 g, 29.2 mmol) then the solids were suspended in N-methylpyrrolidinone (28.5 mL). The mixture was heated to 90 °C for 14 hours then stirred at ambient temperature for 34 hours. The reaction mixture was diluted with ethyl acetate and water and the layers were separated. The aqueous was washed with ethyl acetate and the combined organic layers were washed five times with water, saturated NaCl, dried over Na SO and concentrated in vacuo to a cream-colored solid (4.36 g). LCMS ESI (+) m/z (M+H) 418, 420.

Step B: Preparation of 4-((5-chloropyridinyl)oxy) ((difluoromethyl)sulfonyl)-2,3-dihydro-1H-indenone: 3-Chloro((7- ((difluoromethyl)sulfonyl)-2,3-dihydrospiro[indene-1,2'-[1,3]dioxolan]yl)oxy)pyridine (5.07 g, 12.1 mmol) was dissolved in 6:1 acetone / water (100 mL) and treated with pyridinium p-toluenesulfonate (304 mg, 1.21 mmol). The mixture was heated to 82 °C for 22 hours then stirred at ambient temperature for 38 hours. The reaction mixture was treated with additional pyridinium p-toluenesulfonate (304 mg, 1.21 mmol) and reheated to 90 °C for 24 hours. The reaction was cooled and concentrated in vacuo. The remaining aqueous was treated with saturated NaHCO and ethyl acetate then separated. The aqueous was washed with ethyl acetate and the combined organics were washed with saturated NaHCO , saturated NaCl, dried over Na SO and concentrated in vacuo to a tan solid (4.25 g). LCMS ESI (+) m/z (M+H) 374, 376.

Step C: Preparation of N-butyl((5-chloropyridinyl)oxy) ((difluoromethyl)sulfonyl)-2,3-dihydro-1H-indenimine: 4-((5-Chloropyridinyl)oxy) ((difluoromethyl)sulfonyl)-2,3-dihydro-1H-indenone (4.25 g, 11.4 mmol) was suspended in benzene (250 mL) and treated with butylamine (45 mL, 454 mmol) and trifluoroacetic acid (0.44 mL, 5.7 mmol). The reaction flask was heated through a Dean-Stark trap while monitoring the reaction by H NMR. After 3.5 hours, the reaction mixture was cooled and concentrated in vacuo then the residue was redissolved in MTBE and water. After separation, the organic layer was washed three times with water, saturated NaHCO , saturated NaCl, dried over Na SO and concentrated in vacuo to a tan solid (4.8 g).

Step D: Preparation of 4-((5-chloropyridinyl)oxy) ((difluoromethyl)sulfonyl)-2,2-difluoro-2,3-dihydro-1H-indenone: N-Butyl((5- chloropyridinyl)oxy)((difluoromethyl)sulfonyl)-2,3-dihydro-1H-indenimine (4.8 g, 11.2 mmol) was dissolved in dry acetonitrile (110 mL) and treated with Selectfluor (9.9 g, 28 mmol) and sodium sulfate (16 g, 112 mmol). The mixture was heated to 100 °C for 8 hours then stirred for 3 hours at ambient temperature. The mixture was treated with concentrated aqueous HCl (14 mL, 169 mmol) and stirred for 10 minutes. The mixture was concentrated in vacuo then the resulting suspension was diluted with water (250 mL) and ethyl acetate. After separation, the aqueous was washed twice with ethyl acetate and the combined organic layer was washed with saturated NaHCO , saturated NaCl, dried over Na2SO4 and concentrated in vacuo to a dark semi-solid. The crude product was redissolved in methylene chloride and chromatographed on SiO eluting with a gradient of ethyl acetate/hexane. The desired material was collected and concentrated in vacuo to a cream- colored solid (1.76 g). LCMS ESI (+) m/z (M+H) 409.