WO2007056341A1 - Heterocyclic modulators of atp-binding cassette transporters - Google Patents

Heterocyclic modulators of atp-binding cassette transporters Download PDF

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Publication number
WO2007056341A1
WO2007056341A1 PCT/US2006/043289 US2006043289W WO2007056341A1 WO 2007056341 A1 WO2007056341 A1 WO 2007056341A1 US 2006043289 W US2006043289 W US 2006043289W WO 2007056341 A1 WO2007056341 A1 WO 2007056341A1
Authority
WO
WIPO (PCT)
Prior art keywords
optionally substituted
compound according
aliphatic
independently
heteroaryl
Prior art date
Application number
PCT/US2006/043289
Other languages
French (fr)
Inventor
Sara Hadida Ruah
Matthew Hamilton
Mark Miller
Peter D. J. Grootenhuis
Brian Bear
Jason Mccarthy
Jinglan Zhou
Original Assignee
Vertex Pharmaceuticals Incorporated
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=37766297&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2007056341(A1) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority to DK06837028.7T priority Critical patent/DK1945632T3/en
Priority to KR1020137007108A priority patent/KR20130034062A/en
Priority to CA2627358A priority patent/CA2627358C/en
Application filed by Vertex Pharmaceuticals Incorporated filed Critical Vertex Pharmaceuticals Incorporated
Priority to EP20150602.9A priority patent/EP3696174A1/en
Priority to PL06837028T priority patent/PL1945632T3/en
Priority to EP16205718.6A priority patent/EP3208272B1/en
Priority to CN2006800505211A priority patent/CN101356170B/en
Priority to KR1020157007929A priority patent/KR20150041174A/en
Priority to KR1020087013765A priority patent/KR101331768B1/en
Priority to AU2006311650A priority patent/AU2006311650B2/en
Priority to ES06837028.7T priority patent/ES2439736T3/en
Priority to SI200631716T priority patent/SI1945632T1/en
Priority to KR1020167014530A priority patent/KR20160067985A/en
Priority to EP06837028.7A priority patent/EP1945632B1/en
Priority to NZ567892A priority patent/NZ567892A/en
Priority to KR1020137032983A priority patent/KR101561482B1/en
Priority to JP2008540115A priority patent/JP5317184B2/en
Priority to KR1020137007109A priority patent/KR20130042034A/en
Publication of WO2007056341A1 publication Critical patent/WO2007056341A1/en
Priority to IL191141A priority patent/IL191141A/en
Priority to US12/114,935 priority patent/US8993600B2/en
Priority to NO20082674A priority patent/NO20082674L/en
Priority to HK09103553.4A priority patent/HK1125366A1/en
Priority to US13/475,388 priority patent/US20120232059A1/en
Priority to IL222784A priority patent/IL222784A/en
Priority to US13/871,356 priority patent/US8741933B2/en
Priority to US13/871,349 priority patent/US20130245010A1/en
Priority to US13/871,364 priority patent/US9216969B2/en
Priority to US14/484,192 priority patent/US20150065500A1/en
Priority to US14/925,804 priority patent/US20160143898A1/en
Priority to US15/170,263 priority patent/US20180282311A9/en
Priority to US16/197,732 priority patent/US10626111B2/en
Priority to US16/789,945 priority patent/US11084804B2/en
Priority to US17/362,597 priority patent/US20220153729A1/en

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6872—Intracellular protein regulatory factors and their receptors, e.g. including ion channels
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    • C07D317/10—Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3 not condensed with other rings
    • C07D317/12—Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3 not condensed with other rings with only hydrogen atoms or radicals containing only hydrogen and carbon atoms, directly attached to ring carbon atoms
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
    • C07D405/02—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings
    • C07D405/12—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings linked by a chain containing hetero atoms as chain links
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
    • C07D405/14—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing three or more hetero rings
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4712—Cystic fibrosis

Definitions

  • the present invention relates to modulators of ATP-Binding Cassette
  • ABC Cystic Fibrosis Transmembrane Conductance Regulator
  • CFTR Cystic Fibrosis Transmembrane Conductance Regulator
  • ABC transporters are a family of membrane transporter proteins that regulate the transport of a wide variety of pharmacological agents, potentially toxic drugs, and xenobiotics, as well as anions.
  • ABC transporters are homologous membrane proteins that bind and use cellular adenosine triphosphate (ATP) for their specific activities. Some of these transporters were discovered as multi-drug resistance proteins (like the MDRl-P glycoprotein, or the multi-drug resistance protein, MRPl), defending malignant cancer cells against chemotherapeutic agents. To date, 48 ABC Transporters have been identified and grouped into 7 families based on their sequence identity and function.
  • ABC transporters regulate a variety of important physiological roles within the body and provide defense against harmful environmental compounds. Because of this, they represent important potential drug targets for the treatment of diseases associated with defects in the transporter, prevention of drug transport out of the target cell, and intervention in other diseases in which modulation of ABC transporter activity may be beneficial.
  • CFTR cAMP/ATP-mediated anion channel
  • CFTR is expressed in a variety of cells types, including absorptive and secretory epithelia cells, where it regulates anion flux across the membrane, as well as the activity of other ion channels and proteins. In epithelia cells, normal functioning of CFTR is critical for the maintenance of electrolyte transport throughout the body, including respiratory and digestive tissue.
  • CFTR is composed of approximately 1480 amino acids that encode a protein made up of a tandem repeat of transmembrane domains, each containing six transmembrane helices and a nucleotide binding domain. The two transmembrane domains are linked by a large, polar, regulatory (R)-domain with multiple phosphorylation sites that regulate channel activity and cellular trafficking.
  • Cystic Fibrosis affects approximately one in every 2,500 infants in the United States. Within the general United States population, up to 10 million people carry a single copy of the defective gene without apparent ill effects. In contrast, individuals with two copies of the CF associated gene suffer from the debilitating and fatal effects of CF, including chronic lung disease.
  • the most prevalent mutation is a deletion of phenylalanine at position 508 of the CFTR amino acid sequence, and is commonly referred to as ⁇ F508-CFTR.
  • This mutation occurs in approximately 70% of the cases of cystic fibrosis and is associated with a severe disease.
  • the deletion of residue 508 in ⁇ F508-CFTR prevents the nascent protein from folding correctly. This results in the inability of the mutant protein to exit the ER, and traffic to the plasma membrane. As a result, the number of channels present in the membrane is far less than observed in cells expressing wild-type CFTR. In addition to impaired trafficking, the mutation results in defective channel gating.
  • CFTR transports a variety of molecules in addition to anions
  • this role represents one element in an important mechanism of transporting ions and water across the epithelium.
  • the other elements include the epithelial Na + channel, ENaC, Na + /2C17K + co-transporter, Na + -K + -ATPaSe pump and the basolateral membrane K + channels, that are responsible for the uptake of chloride into the cell.
  • COPD chronic obstructive pulmonary disease
  • COPD dry eye disease
  • Sjogren's Syndrome Sjogren's Syndrome
  • COPD chronic obstructive pulmonary disease
  • Activators of mutant or wild-type CFTR offer a potential treatment of mucus hypersecretion and impaired mucociliary clearance that is common in COPD.
  • CFTR Dry eye disease
  • tear aqueous production and abnormal tear film lipid, protein and mucin profiles There are many causes of dry eye, some of which include age, Lasik eye surgery, arthritis, medications, chemical/thermal burns, allergies, and diseases, such as Cystic Fibrosis and Sj ⁇ grens's syndrome.
  • Increasing anion secretion via CFTR would enhance fluid transport from the corneal endothelial cells and secretory glands surrounding the eye to increase corneal hydration.
  • Sj ⁇ grens's syndrome is an autoimmune disease in which the immune system attacks moisture-producing glands throughout the body, including the eye, mouth, skin, respiratory tissue, liver, vagina, and gut. Symptoms, include, dry eye, mouth, and vagina, as well as lung disease. The disease is also associated with rheumatoid arthritis, systemic lupus, systemic sclerosis, and polymypositis/dermatomyositis. Defective protein trafficking is believed to cause the disease, for which treatment options are limited. Modulators of CFTR activity may hydrate the various organs afflicted by the disease and help to elevate the associated symptoms.
  • ⁇ F508-CFTR prevents the nascent protein from folding correctly, resulting in the inability of this mutant protein to exit the ER, and traffic to the plasma membrane.
  • insufficient amounts of the mature protein are present at the plasma membrane and chloride transport within epithelial tissues is significantly reduced.
  • this cellular phenomenon of defective ER processing of ABC transporters by the ER machinery has been shown to be the underlying basis not only for CF disease, but for a wide range of other isolated and inherited diseases.
  • the diseases associated with the first class of ER malfunction are Cystic fibrosis (due to misfolded ⁇ F508-CFTR as discussed above), Hereditary emphysema (due to al-antitrypsin; non Piz variants), Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses (due to Lysosomal processing enzymes), Sandhof/Tay-Sachs (due to ⁇ - Hexosaminidase), Crigler-Najjar type II (due to UDP-glucuronyl-sialyc-transferase), Polyendoc
  • Glycanosis CDG type 1 Hereditary emphysema (due to ⁇ l -Antitrypsin (PiZ variant), Congenital hyperthyroidism, Osteogenesis imperfecta (due to Type I, II, IV procollagen), Hereditary hypofibrinogenemia (due to Fibrinogen), ACT deficiency (due to ⁇ l-Antichymotrypsin), Diabetes insipidus (DI), Neurophyseal DI (due to Vasopvessin hormone/ V2-receptor), Neprogenic DI (due to Aquaporin II), Charcot-Marie Tooth syndrome (due to Peripheral myelin protein 22), Perlizaeus- Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease ( due to ⁇ APP and presenilins), Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick
  • CFTR modulators may be beneficial for the treatment of secretory diarrheas, in which epithelial water transport is dramatically increased as a result of secretagogue activated chloride transport.
  • the mechanism involves elevation of cAMP and stimulation of CFTR.
  • Acute and chronic diarrheas represent a major medical problem in many areas of the world. Diarrhea is both a significant factor in malnutrition and the leading cause of death (5,000,000 deaths/year) in children less than five years old. [00117] ⁇ Secretory diarrheas are also a dangerous condition in patients of acquired immunodeficiency syndrome (ADDS) and chronic inflammatory bowel disease (EBD). 16 million travelers to developing countries from industrialized nations every year develop diarrhea, with the severity and number of cases of diarrhea varying depending on the country and area of travel.
  • ADDS acquired immunodeficiency syndrome
  • EBD chronic inflammatory bowel disease
  • Diarrhea in barn animals and pets such as cows, pigs, and horses, sheep, goats, cats and dogs, also known as scours, is a major cause of death in these animals. Diarrhea can result from any major transition, such as weaning or physical movement, as well as in response to a variety of bacterial or viral infections and generally occurs within the first few hours of the animal's life.
  • ETEC having the K99 pilus antigen.
  • Common viral causes of diarrhea include rotavirus and coronavirus.
  • Other infectious agents include Cryptosporidium, giardia lamblia, and salmonella, among others.
  • Symptoms of rotaviral infection include excretion of watery feces, dehydration and weakness. Coronavirus causes a more severe illness in the newborn animals, and has a higher mortality rate than rotaviral infection. Often, however, a young animal may be infected with more than one virus or with a combination of viral and bacterial microorganisms at one time. This dramatically increases the severity of the disease.
  • cystic fibrosis hereditary emphysema, hereditary hemochromatosis, coagulation-fibrinolysis deficiencies, such as protein C deficiency, Type 1 hereditary angioedema, lipid processing deficiencies, such as familial hypercholesterolemia, Type 1 chylomicronemia, abetalipoproteinemia, lysosomal storage diseases, such as I-cell disease/pseudo-Hurler, mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, polyendocrinopathy/hyperinsulemia, Diabetes Mellitus, Laron dwarfism, myleoperoxidase deficiency, primary hypoparathyroidism, melanoma, glycanosis CDG type 1, her
  • ABC-transporter as used herein means an ABC-transporter protein or a fragment thereof comprising at least one binding domain, wherein said protein or fragment thereof is present in vivo or in vitro.
  • binding domain as used herein means a domain on the ABC-transporter that can bind to a modulator. See, e.g., Hwang, T. C. et al., J. Gen. Physiol. (1998): 111(3), 477-90.
  • CFTR cystic fibrosis transmembrane conductance regulator or a mutation thereof capable of regulator activity, including, but not limited to, ⁇ F508 CFTR and G551D CFTR (see, e.g., http://www.genet.sickkids.on.ca/cftr/, for CFTR mutations).
  • modulating means increasing or decreasing, e.g. activity, by a measurable amount.
  • Compounds that modulate ABC Transporter activity, such as CFTR activity, by increasing the activity of the ABC Transporter, e.g., a CFTR anion channel are called agonists.
  • Compounds that modulate ABC Transporter activity, such as CFTR activity, by decreasing the activity of the ABC Transporter, e.g., CFTR anion channel are called antagonists.
  • An agonist interacts with an ABC Transporter, such as CFTR anion channel, to increase the ability of the receptor to transduce an intracellular signal in response to endogenous ligand binding.
  • An antagonist interacts with an ABC Transporter, such as CFTR, and competes with the endogenous ligand(s) or substrate(s) for binding site(s) on the receptor to decrease the ability of the receptor to transduce an intracellular signal in response to endogenous ligand binding.
  • ABC Transporter such as CFTR
  • the phrase "treating or reducing the severity of an ABC Transporter mediated disease” refers both to treatments for diseases that are directly caused by ABC Transporter and/or CFTR activities and alleviation of symptoms of diseases not directly caused by ABC Transporter and/or CFTR anion channel activities.
  • diseases whose symptoms may be affected by ABC Transporter and/or CFTR activity include, but are not limited to, Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation- Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1, Hereditary emphysema, Con
  • aliphatic encompasses the terms alkyl, alkenyl, alkynyl, each of which being optionally substituted as set forth below.
  • an "alkyl” group refers to a saturated aliphatic hydrocarbon group containing 1-8 (e.g., 1-6 or 1-4) carbon atoms.
  • An alkyl group can be straight or branched. Examples of alkyl groups include, but are not limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, n-heptyl, or 2-ethylhexyl.
  • An alkyl group can be substituted (i.e., optionally substituted) with one or more substituents such as halo, cycloaliphatic [e.g., cycloalkyl or cycloalkenyl], heterocycloaliphatic [e.g., heterocycloalkyl or heterocycloalkenyl], aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, acyl [e.g., (aliphatic)c.arbonyl, (cycloaliphatic)carbonyl, or (heterocycloaliphatic)carbonyl], nitro, cyano, amido [e.g., (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, heteroaral
  • substituted alkyls include carboxyalkyl (such as HOOC-alkyl, alkoxycarbonylalkyl, and alkylcarbonyloxyalkyl), cyanoalkyl, hydroxyalkyl, alkoxyalkyl, acylalkyl, hydroxyalkyl, aralkyl, (alkoxyaryl)alkyl, (sulfonylamino)alkyl (such as (alkylsulfonylamino)alkyl), aminoalkyl, amidoalkyl, (cycloaliphatic)alkyl, cyanoalkyl, or haloalkyl.
  • carboxyalkyl such as HOOC-alkyl, alkoxycarbonylalkyl, and alkylcarbonyloxyalkyl
  • cyanoalkyl such as HOOC-alkyl, alkoxycarbonylalkyl, and alkylcarbonyloxyalkyl
  • cyanoalkyl such as HO
  • an "alkenyl” group refers to an aliphatic carbon group that contains 2-8 (e.g., 2-6 or 2-4) carbon atoms and at least one double bond. Like an alkyl group, an alkenyl group can be straight or branched. Examples of an alkenyl group include, but are not limited to, allyl, isoprenyl, 2-butenyl, and 2-hexenyl.
  • An alkenyl group can be optionally substituted with one or more substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, acyl [e.g., (cycloaliphatic)carbonyl, or (heterocycloaliphatic)carbonyl], nitro, cyano, acyl [e.g., aliphaticcarbonyl, cycloaliphaticcarbonyl, arylcarbonyl, heterocycloaliphaticcarbonyl or heteroarylcarbonyl], amido [e.g., (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino,
  • substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, alkoxy, aroy
  • heterocycloalkylalkyl carbonylamino, heteroarylcarbonylamino, heteroaralkylcarbonylamino alkylaminocarbonyl, cycloalkylaminocarbonyl, heterocycloalkylaminocarbonyl, arylaminocarbonyl, or heteroarylaminocarbonyl] amino [e.g., aliphaticamino, or aliphaticsulfonylamino], sulfonyl [e.g., alkylsulfonyl, cycloaliphaticsulfonyl, or arylsulfonyl], sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, cycloaliphaticoxy, heterocycloaliphaticoxy, aryloxy, heteroaryloxy, aralkyloxy
  • an "alkynyl” group refers to an aliphatic carbon group that contains 2-8 (e.g., 2-6 or 2-4) carbon atoms and has at least one triple bond.
  • An alkynyl group can be straight or branched. Examples of an alkynyl group include, but are not limited to, propargyl and butynyl.
  • An alkynyl group can be optionally substituted with one or more substituents such as aroyl, heteroaroyl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, nitro, carboxy, cyano, halo, hydroxy, sulfo, mercapto, sulfanyl [e.g., aliphaticsulfanyl or cycloaliphaticsulfanyl], sulfinyl [e.g., aliphaticsulfinyl or cycloaliphaticsulfinyl], sulfonyl [e.g., aliphaticsulfonyl, aliphaticaminosulfonyl, or cycloaliphaticsulfonyl], amido [e.g., aminocarbonyl, alkylaminocarbonyl, alkylcarbonylamino, cycloalkylaminocarbony
  • an “amido” encompasses both “aminocarbonyl” and
  • carbonylamino when used alone or in connection with another group refers to an amido group such as N(R X R Y )-C(O)- or R Y C(O)-N(R X )- when used terminally and -C(O)- N(R X )- or -N(R X )-C(O)- when used internally, wherein R x and R ⁇ are defined below.
  • amido groups include alkylamido (such as alkylcarbonylamino or alkylcarbonylamino), (heterocycloaliphatic)amido, (heteroaralkyl)amido, (heteroaryl)amido, (heterocycloalkyl)alkylamido, arylamido, aralkylamido, (cycloalkyl)alkylamido, or cycloalkylamido.
  • alkylamido such as alkylcarbonylamino or alkylcarbonylamino
  • heterocycloaliphatic such as alkylcarbonylamino or alkylcarbonylamino
  • heteroaryl heteroaryl
  • an "amino" group refers to -NR R wherein each of R and R ⁇ is independently hydrogen, alkyl, cycloaliphatic, (cycloaliphatic)aliphatic, aryl, araliphatic, heterocycloaliphatic, (heterocycloaliphatic)aliphatic, heteroaryl, carboxy, sulfanyl, sulfinyl, sulfonyl, (aliphatic)carbonyl, (cycloaliphatic)carbonyl, ((cycloaliphatic)aliphatic)carbonyl, arylcarbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, (heteroaryl)carbonyl, or (heteroaraliphatic)carbonyl, each of which being defined herein and being optionally substituted.
  • amino groups examples include alkylamino, dialkylamino, or arylamino.
  • amino When the term “amino” is not the terminal group (e.g., alkylcarbonylamino), it is represented by - NR X -. R x has the same meaning as defined above.
  • an "aryl” group used alone or as part of a larger moiety as in “aralkyl”, “aralkoxy”, or “aryloxyalkyl” refers to monocyclic (e.g., phenyl); bicyclic (e.g., indenyl, naphthalenyl, tetrahydronaphthyl, tetrahydroindenyl); and tricyclic (e.g., fluorenyl tetrahydrofluorenyl, or tetrahydroanthracenyl, anthracenyl) ring systems in which the monocyclic ring system is aromatic or at least one of the rings in a bicyclic or tricyclic ring system is aromatic.
  • the bicyclic and tricyclic ring systems include benzofused 2-3 membered carbocyclic rings.
  • a benzofused group includes phenyl fused with two or more C 4- 8 carbocyclic moieties.
  • An aryl is optionally substituted with one or more substituents including aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliphatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic ring of a benzofused bicyclic or tricyclic aryl); nitro
  • Non-limiting examples of substituted aryls include haloaryl [e.g., mono-, di ( such as/VTz-dihaloaryl), and (trihalo)aryl]; (carboxy)aryl [e.g., (alkoxycarbonyl)aryl, ((aralkyi)carbonyloxy)aryl, and (alkoxycarbonyl)aryl]; (amido)aryl [e.g., (aminocarbonyl)aryl, (((alkylamino)a ⁇ kyl)aminocarbonyl)aryl, (alkylcarbonyl)aminoaryl, (arylaminocarbonyl)aryl, and (((heteroaryl)amino)carbonyl)aryl]; aminoaryl [e.g., ((alkylsulfonyl)amino)aryl or ((dialkyl)amino)aryl]; (cyanoalkyl)aryl;
  • an "araliphatic” such as an “aralkyl” group refers to an aliphatic group (e.g., a Ci -4 alkyl group) that is substituted with an aryl group.
  • "Aliphatic,” “alkyl,” and “aryl” are defined herein.
  • An example of an araliphatic such as an aralkyl group is benzyl.
  • an "aralkyl” group refers to an alkyl group (e.g., a Ci -4 alkyl group) that is substituted with an aryl group. Both “alkyl” and “aryl” have been defined above. An example of an aralkyl group is benzyl.
  • An aralkyl is optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl, including carboxyalkyl, hydroxyalkyl, or haloalkyl such as trifluoromethyl], cycloaliphatic [e.g., cycloalkyl or cycloalkenyl], (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, amido [e.g., aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylarnino, (cyclo
  • a "bicyclic ring system” includes 8-12 (e.g., 9, 10, or 11) membered structures that form two rings, wherein the two rings have at least one atom in common (e.g., 2 atoms in common).
  • Bicyclic ring systems include bicycloaliphatics (e.g., bicycloalkyl or bicycloalkenyl), bicycloheteroaliphatics, bicyclic aryls, and bicyclic heteroaryls.
  • a "cycloaliphatic” group encompasses a “cycloalkyl” group and a “cycloalkenyl” group, each of which being optionally substituted as set forth below.
  • a "cycloalkyl” group refers to a saturated carbocyclic mono- or bicyclic (fused or bridged) ring of 3-10 (e.g., 5-10) carbon atoms.
  • Examples of cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, norbornyl, cubyl, octahydro-indenyl, decahydro-naphthyl, bicyclo[3.2.1]octyl, bicyclo[2.2.2]octyl, bicyclo[3.3.1]nonyl, bicyclo[3.3.2.]decyl, bicyclo[2.2.2]octyl, adamantyl, azacycloalkyl, or ((aminocarbonyl)cycloalkyl)cycloalkyl.
  • a "cycloalkenyl” group refers to a non-aromatic carbocyclic ring of 3-10 (e.g., 4-8) carbon atoms having one or more double bonds.
  • Examples of cycloalkenyl groups include cyclopentenyl, 1,4-cyclohexa-di- enyl, cycloheptenyl, cyclooctenyl, hexahydro-indenyl, octahydro-naphthyl, cyclohexenyl, cyclopentenyl, bicyclo[2.2.2]octenyl, or bicyclo[3.3.1]nonenyl.
  • a cycloalkyl or cycloalkenyl group can be optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic) aliphatic, heterocycloaliphatic, (heterocycloaliphatic) aliphatic, aryl, heteroaryl, alkoxy, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliphatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic )carbonylamino,
  • substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic) aliphatic, heterocycloaliphatic, (hetero
  • cycloaliphatic)carbonylamino ((cycloaliphatic)aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (heterocycloaliphatic)carbonylamino, ((heterocycloaliphatic)aliphatic)carbonylamino, (heteroaryl)carbonylamino, or (heteroaraliphatic)carbonylamino], nitro, carboxy [e.g., HOOC-, alkoxycarbonyl, or alkylcarbonyloxy], acyl [e.g., (cycloali ⁇ hatic)carbonyl, ((cycloaliphatic) aliphatic)carbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, or (heteroaraliphatic)carbonyl], cyano, halo, hydroxy,
  • cyclic moiety includes cycloaliphatic, heterocycloaliphatic, aryl, or heteroaryl, each of which has been defined previously.
  • heterocycloaliphatic encompasses a heterocycloalkyl group and a heterocycloalkenyl group, each of which being optionally substituted as set forth below.
  • heterocycloalkyl refers to a 3-10 membered mono- or bicylic (fused or bridged) (e.g., 5- to 10-membered mono- or bicyclic) saturated ring structure, in which one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof).
  • heterocycloalkyl group examples include piperidyl, piperazyl, tetrahydropyranyl, tetrahydrofuryl, 1,4-dioxolanyl, 1,4-dithianyl, 1,3-dioxoIanyl, oxazolidyl, isoxazolidyl, morpholinyl, thiomorpholyl, octatvydrobenzofuryl, octahydrochromenyl, octahydrothiochromenyl, octahydroindolyl, octahydropyrindinyl, decahydroquinolinyl, octahydrobenzo[&]thiopheneyl, 2-oxa-bicyclo[2.2.2]octyl, l-aza-bicyclo[2.2.2]octyl, 3-aza- bicyclo[3.2.1]octyl, and 2,6-d
  • a monocyclic heterocycloalkyl group can be fused with a phenyl moiety such as tetrahydroisoquinoline.
  • a "heterocycloalkenyl” group refers to a mono- or bicylic (e.g., 5- to 10- membered mono- or bicyclic) non-aromatic ring structure having one or more double bonds, and wherein one or more of the ring atoms is a heteroatom (e.g., N, O, or S).
  • Monocyclic and bicycloheteroaliphatics are numbered according to standard chemical nomenclature.
  • a heterocycloalkyl or heterocycloalkenyl group can be optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic)ali ⁇ hatic, heterocycloaliphatic, (heterocycloaliphatic)aliphatic, aryl, heteroaryl, alkoxy, (cycloali ⁇ hatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroarali ⁇ hatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic)carbonylamino, (cycloaliphatic)carbonylarnino, ((cycloaliphatic) aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (hetero
  • a “heteroaryl” group refers to a monocyclic, bicyclic, or tricyclic ring system having 4 to 15 ring atoms wherein one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof) and in which the monocyclic ring system is aromatic or at least one of the rings in the bicyclic or tricyclic ring systems is aromatic.
  • a heteroaryl group includes a benzofused ring system having 2 to 3 rings.
  • a benzofused group includes benzo fused with one or two 4 to S rnembered heterocycloaliphatic moieties (e.g., indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo[ib]furyl, benzo[&]thiophenyl, quinolinyl, or isoquinolinyl).
  • 4 to S rnembered heterocycloaliphatic moieties e.g., indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo[ib]furyl, benzo[&]thiophenyl, quinolinyl, or isoquinolinyl.
  • heteroaryl examples include azetidinyl, pyridyl, lH-indazolyl, furyl, pyrrolyl, thienyl, thiazolyl, oxazolyl, ir ⁇ idazolyl, tetrazolyl, benzofuryl, isoquinolinyl, benzthiazolyl, xanthene, thioxanthene, phenothiazine, dihydroindole, benzo[l,3]dioxole, benzo[b]furyl, benzo[b]thiophenyl, indazolyl, benzimidazolyl, benzthiazolyl, puryl, cinnolyl, quinolyl, quinazolyl,cinnolyl, phthalazyl, quinazolyl, quinoxalyl, isoquinolyl, 4H-quinolizyl, benzo-l,2,5-thi
  • monocyclic heteroaryls include furyl, thiophenyl, 2H- pyrrolyl, pyrrolyl, oxazolyl, thazolyl, imidazolyl, pyrazolyl, isoxazolyl, isothiazolyl, 1,3,4- thiadiazolyl, 2H-pyranyl, 4-H-pyranyl, pyridyl, pyridazyl, pyrimidyl, pyrazolyl, pyrazyl, or 1,3,5-triazyl.
  • Monocyclic heteroaryls are numbered according to standard chemical nomenclature.
  • bicyclic heteroaryls include indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo [6]furyl, benzo[ ⁇ ]thiophenyl, quinolinyl, isoquinolinyl, indolizyl, isoindolyl, indolyl, benzo[&]furyl, be ⁇ o[£]thio ⁇ henyl, indazolyl, benzimidazyl, benzthiazolyl, purinyl, 4H-quinolizyl, quinolyl, isoquinolyl, cinnolyl, phthalazyl, quinazolyl, quinoxalyl, 1,8-naphthyridyl, or pteridyl.
  • Bicyclic heteroaryls are numbered according to standard chemical nomenclature.
  • a heteroaryl is optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloali ⁇ hatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic or heterocyclic ring of a bicyclic or tricyclic heteroaryl); carboxy; amido; acyl [ e.g., aliphaticcarbonyl; (cycloaliphatic)carbonyl; ((cycloaliphatic)ali ⁇ hatic)carbonyl; (araliphathat
  • substituted heteroaryls include (halo)heteroaryl
  • heteroaralkyl refers to an aliphatic group (e.g., a C 1-4 alkyl group) that is substituted with a heteroaryl group.
  • aliphatic group e.g., a C 1-4 alkyl group
  • heteroaryl e.g., a C 1-4 alkyl group
  • a "heteroaralkyl” group refers to an alkyl group (e.g., a
  • a heteroaralkyl is optionally substituted with one or more substituents such as alkyl (including carboxyalkyl, hydroxyalkyl, and haloalkyl such as trifluoromethyl), alkenyl, alkynyl, cycloalkyl, (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylamino, (cycloalkyl)
  • an "acyl” group refers to a formyl group or R X -C(O)-
  • alkylcarbonyl (such as -alkyl-C(O)-, also referred to as “alkylcarbonyl”) where R x and "alkyl” have been defined previously.
  • Acetyl and pivaloyl are examples of acyl groups.
  • an "aroyl” or “heteroaroyl” refers to an aryl-C(O)- or a heteroaryl-C(O)-.
  • the aryl and heteroaryl portion of the aroyl or heteroaroyl is optionally substituted as previously defined.
  • an "alkoxy” group refers to an alkyl-O- group
  • alkyl has been defined previously.
  • a "carbamoyl” group refers to a group having the structure -O-CO-NR X R Y or -NR X -CO-O-R Z wherein R x and R ⁇ have been defined above and R can be aliphatic, aryl, araliphatic, heterocycloaliphatic, heteroaryl, or heteroaraliphatic.
  • a "carboxy” group refers to -COOH, -COOR X , -OC(O)H,
  • haloaliphatic refers to an aliphatic group substituted with 1, 2, or 3 halogen.
  • haloalkyl includes the group -CF 3 .
  • mercapto refers to -SH.
  • a "sulfo" group refers to -SO 3 H or -SO 3 R X when used terminally or -S(O) 3 - when used internally.
  • sulf amide refers to the structure -NR X -S(O) 2 -
  • a "sulfamoyl” group refers to the structure -S(O) 2 -NR X R Y or -NR X -S (O) 2 -R 2 when used terminally; or -S(O) 2 -NR X - or -NR X -S(O) 2 - when used internally, wherein R x , R ⁇ , and R z are defined above.
  • a "sulfanyl” group refers to -S-R x when used terminally and -S- when used internally, wherein R x has been defined above. Examples of sulfanyls include alkylsulfanyl.
  • a "sulfinyl” group refers to -S(O)-R X when used terminally and -S(O)- when used internally, wherein R x has been defined above.
  • a "sulfonyl” group refers to-S(O) 2 -R x when used terminally and -S(O) 2 - when used internally, wherein R has been defined above.
  • a "sulfoxy" group refers to -O-SO-R X or -SO-O-R X , when used terminally and -0-S(O)- or -S(O)-O- when used internally, where R has been defined above.
  • halogen or halo group refers to fluorine, chlorine, bromine or iodine.
  • alkoxycarbonyl which is encompassed by the term carboxy, used alone or in connection with another group refers to a group such as alkyl-O-C(O)-
  • alkoxyalkyl refers to an alkyl group such as alkyl-O- alkyl-, wherein alkyl has been defined above.
  • aminoalkyl refers to the structure (R x R Y )N-alkyl-.
  • cyanoalkyl refers to the structure (NC)-alkyl-.
  • a "urea” group refers to the structure -NR X -CO-NR Y R Z and a “thiourea” group refers to the structure -NR X -CS-NR Y R Z when used terminally and -NR X - CO-NR Y - or -NR X -CS-NR Y - when used internally, wherein R x , R ⁇ , and R z have been defined above.
  • amino refers to the structure -
  • the term "vicinal” refers to the placement of substituents on a group that includes two or more carbon atoms, wherein the substituents are attached to adjacent carbon atoms.
  • the term "geminal” refers to the placement of substituents on a group that includes two or more carbon atoms,- wherein the substituents are attached to the same carbon atom.
  • terminal refers to the location of a group within a substituent.
  • a group is terminal when the group is present at the end of the substituent not further bonded to the rest of the chemical structure.
  • Carboxyalkyl i.e., R x O(O)C-alkyl is an example of a carboxy group used terminally.
  • a group is internal when the group is present in the middle of a substituent to at the end of the substituent bound to the rest of the chemical structure.
  • Alkylcarboxy e.g., alkyl-C(O)O- or alkyl-OC(O)-
  • alkylcarboxyaryl e.g., alkyl- C(O)O-aryl- or alkyl-O(CO)-aryl-
  • cyclic group includes mono-, bi-, and tri-cyclic ring systems including cycloaliphatic, heterocycloaliphatic, aryl, or heteroaryl, each of which has been previously defined.
  • bridged bicyclic ring system refers to a bicyclic heterocyclicalipahtic ring system or bicyclic cycloaliphatic ring system in which the rings are bridged.
  • bridged bicyclic ring systems include, but are not limited to, adamantanyl, norbornanyl, bicyclo[3.2.1]octyl, bicyclo[2.2.2]octyl, bicyclo[3.3.1]nonyl, bicyclo[3.2.3]nonyl, 2-oxa-bicyclo[2.2.2]octyl, l-aza-bicyclo[2.2.2]octyl, 3-aza- bicyclo[3.2.1]octyl, and 2,6-dioxa-tricyclo[3.3.1.03,7]nonyl.
  • a bridged bicyclic ring system can be optionally substituted with one or more substituents such as alkyl (including carboxyalkyl, hydroxyalkyl, and haloalkyl such as trifluoromethyl), alkenyl, alkynyl, cycloalkyl, (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylamino, (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heter
  • an "aliphatic chain” refers to a branched or straight aliphatic group (e.g., alkyl groups, alkenyl groups, or alkynyl groups).
  • a straight aliphatic chain has the structure -[CH 2 ] V -, where v is 1-6.
  • a branched aliphatic chain is a straight aliphatic chain that is substituted with one or more aliphatic groups.
  • a branched aliphatic chain has the structure -[CHQ] V - where Q is hydrogen or an aliphatic group; however, Q shall be an aliphatic group in at least one instance.
  • the term aliphatic chain includes alkyl chains, alkenyl chains, and alkynyl chains, where alkyl, alkenyl, and alkynyl are defined above.
  • Each substituent of a specific group is further optionally substituted with one to three of halo, cyano, oxoalkoxy, hydroxy, amino, nitro, aryl, haloalkyl, and alkyl.
  • an alkyl group can be substituted with alkylsulfanyl and the alkylsulfanyl can be optionally substituted with one to three of halo, cyano, oxoalkoxy, hydroxy, amino, nitro, aryl, haloalkyl, and alkyl.
  • the cycloalkyl portion of a (cycloalkyl)carbonylamino can be optionally substituted with one to three of halo, cyano, alkoxy, hydroxy, nitro, haloalkyl, and alkyl.
  • the two alkoxy groups can form a ring together with the atom(s) to which they are bound.
  • an optionally substituted group can have a substituent at each substitutable position of the group, and when more than one position in any given structure can be substituted with more than one substituent selected from a specified group, the substituent can be either the same or different at every position.
  • a ring substituent such as a heterocycloalkyl, can be bound to another ring, such as a cycloalkyl, to form a spiro-bicyclic ring system, e.g., both rings share one common atom.
  • substituents envisioned by this invention are those combinations that result in the formation of stable or chemically feasible compounds.
  • stable or chemically feasible refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and preferably their recovery, purification, and use for one or more of the purposes disclosed herein.
  • a stable compound or chemically feasible compound is one that is not substantially altered when kept at a temperature of 40° C or less, in the absence of moisture or other chemically reactive conditions, for at least a week.
  • an effective amount is defined as the amount required to confer a therapeutic effect on the treated patient, and is typically determined based on age, surface area, weight, and condition of the patient. The interrelationship of dosages for animals and humans (based on milligrams per meter squared of body surface) is described by Freireich et al., Cancer Chemother. Rep., 50: 219 (1966). Body surface area may be approximately determined from height and weight of the patient. See, e.g., Scientific Tables, Geigy Pharmaceuticals, Ardsley, New York, 537 (1970). As used herein, "patient” refers to a mammal, including a human.
  • structures depicted herein are also meant to include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure; for example, the R and S configurations for each asymmetric center, (Z) and (E) double bond isomers, and (Z) and (E) conformational isomers. Therefore, single stereochemical isomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the invention. Unless otherwise stated, all tautomeric forms of the compounds of the invention are within the scope of the invention.
  • structures depicted herein are also meant to include compounds that differ only in the presence of one or more isotopically enriched atoms.
  • compounds having the present structures except for the replacement of hydrogen by deuterium or tritium, or the replacement of a carbon by a 1 C- or 14 C ⁇ enriched carbon are within the scope of this invention.
  • Such compounds are useful, for example, as analytical tools or probes in biological assays.
  • Compounds of the present invention are useful modulators of ABC transporters and are useful in the treatment of ABC transport mediated diseases.
  • the present invention includes a compound of formula (I),
  • Each R 1 is an optionally substituted C 1-6 aliphatic, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted C 3- io cycloaliphatic, an optionally substituted 3 to 10 membered heterocycloaliphatic, carboxy [e.g., hydroxycarbonyl or alkoxycarbonyl], amido [e.g., aminocarbonyl], amino, halo, or hydroxy; provided that at least one R 1 is an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl attached to the 5- or 6- position of the pyridyl ring;
  • Each R 2 is hydrogen, an optionally substituted C 1-6 aliphatic, an optionally substituted C 3-6 cycloaliphatic, an optionally substituted phenyl, or an optionally substituted heteroaryl;
  • Each R 3 and R' 3 together with the carbon atom to which they are attached form an optionally substituted C 3-7 cycloaliphatic or an optionally substituted heterocycloaliphatic;
  • Each R 4 is an optionally substituted aryl or an optionally substituted heteroaryl
  • n 1, 2, 3 or 4.
  • the present invention includes compounds of formula
  • G 1 and G 2 are nitrogen, and the other is a carbon;
  • R 1 , R 2 , R 3 , R' 3 , R 4 , and n are defined above.
  • Each R 1 is independently an optionally substituted C 1-6 aliphatic, an optionally substituted ary ⁇ , an optionally substituted heteroaryl, an optionally substituted Cs -1 O membered cycloaliphatic, an optionally substituted 3 to 10 membered heterocycloaliphatic, carboxy [e.g., hydroxycarbonyl or alkoxycarbonyl], amido [e.g., aminocarbonyl], amino, halo, or hydroxy.
  • one R 1 is an optionally substituted C 1-6 aliphatic.
  • one R 1 is an optionally substituted C 1-S alkyl, an optionally substituted C 2-6 alkenyl, or an optionally substituted C2- 6 alkynyl.
  • one Ri is Ci -6 alkyl, C2-6 alkenyl, or C2- 6 alkynyl.
  • one R 1 is an aryl or heteroaryl with 1, 2, or 3 substituents. In several examples, one R 1 is a monocyclic aryl or heteroaryl. In several embodiments, R 1 is an aryl or heteroaryl with 1, 2, or 3 substituents. In several examples, Ri is a monocyclic aryl or heteroaryl.
  • At least one Ri is an optionally substituted aryl or an optionally substituted heteroaryl and R] is bonded to the core structure at the 6 position on the pyridine ring.
  • At least one Ri is an optionally substituted aryl or an optionally substituted heteroaryl and R 1 is bonded to the core structure at the 5 position on the pyridine ring.
  • one R 1 is phenyl with up to 3 substituents. In several embodiments, R 1 is phenyl with up to 3 substituents.
  • one Ri is a heteroaryl ring with up to 3 substituents. In certain embodiments, one Ri is a monocyclic heteroaryl ring with up to 3 substituents. In other embodiments, one Ri is a bicyclic heteroaryl ring with up to 3 substituents. In several embodiments, R 1 is a heteroaryl ring with up to 3 substituents. In certain embodiments, R 1 is a monocyclic heteroaryl ring with up to 3 substituents. In other embodiments, R 1 is a bicyclic heteroaryl ring with up to 3 substituents.
  • one Ri is carboxy [e.g., hydroxycarbonyl or alkoxycarbonyl]. Or, one Ri is amido [e.g., aminocarbonyl]. Or, one Ri is amino. Or, is halo. Or, is cyano. Or, hydroxyl.
  • R 1 is hydrogen, methyl, ethyl, i-propyl, t-butyl, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, allyl, F, Cl, methoxy, ethoxy, i-propoxy, t- butoxy, CF 3 , OCF 3 , CN, hydroxyl, or amino.
  • R 1 is hydrogen, methyl, methoxy, F, CF 3 or OCF 3 .
  • R 1 can be hydrogen.
  • R 1 can be methyl.
  • R 1 can be CF 3 .
  • R 1 can be methoxy.
  • R 1 is substituted with no more than three substituents selected from halo, oxo, or optionally substituted aliphatic, cycloaliphatic, heterocycloaliphatic, amino [e.g., (aliphatic)amino], amido [e.g., aminocarbonyl, ((aliphatic)amino)carbonyl, and ((aliphatic) 2 amino)carbonyl3, carboxy [e.g., alkoxycarbonyl and hydroxycarbonyl], sulfamoyl [e.g., aminosulfonyl, ((aliphatic) 2 amino)sulfonyl, ((cycloaliphatic)aliphatic)aminosulfonyl, and ((cycloaliphatic)amino)sulfonyl], cyano, alkoxy, aryl, heteroaryl [e.g., monocyclic heteroaryl and bicycloheteroaryl], sulfon
  • R 1 is substituted with halo.
  • R 1 substituents include F, Cl, and Br.
  • R 1 is substituted with F.
  • Ri is substituted with an optionally substituted aliphatic.
  • Ri substituents include optionally substituted alkoxyaliphatic, heterocycloaliphatic, aminoalkyl, hydroxyalkyl, (heterocycloalkytyaliphatic, alkylsulfonylaliphatic, alkylsulfonylaminoaliphatic, alkylcarbonylaminoaliphatic, alkylaminoaliphatic, or alkylcarbonylaliphatic.
  • R 1 is substituted with an optionally substituted amino.
  • R 1 substituents include aliphaticcarbonylamino, aliphaticamino, arylamino, or aliphaticsulfonylamino.
  • R 1 is substituted with a sulfonyl.
  • Ri substituents include heterocycloaliphaticsulfonyl, aliphatic sulfonyl, aliphaticaminosulfonyl, aminosulfonyl, aliphaticcarbonylaminosulfonyl, alkoxyalkylheterocycloalkylsulfonyl, alkylheterocycloalkylsulfonyl, alkylaminosulfonyl, cycloalkylaminosulfonyl, (heterocycloalkytyalkylaminosulfonyl, and heterocycloalkylsulfonyl.
  • R 1 is substituted with carboxy.
  • R 1 substituents include alkoxycarbonyl and hydroxycarbonyl.
  • R 1 is substituted with amido.
  • R 1 substituents include alkylaminocarbonyl, aminocarbonyl, ((aliphatic) 2 amino)carbonyl, and [((aliphatic)aminoaliphatic)amino]carbonyl.
  • R 1 is substituted with carbonyl.
  • R 1 substituents include arylca ⁇ bonyl, cycloaliphaticcarbonyl, heterocycloaliphaticcarbonyl, and heteroarylcarbonyl.
  • R 1 is hydrogen. In some embodiments, R 1 is -
  • each Z A is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z A are optionally and independently replaced by -CO-, -CS-, -C0NR A -, -CONR A NR A -, -CO 2 -, -OCO-, -NR A C0 2 -, -O-, - NR A CONR A -, -OCONR A -, -NR A NR A -, -NR A C0-, -S-, -SO-, -SO 2 -, -NR A -, -SO 2 NR A -, - NR A SO 2 -, or -NR A SO 2 NR A -.
  • Each R 5 is independently R A , halo, -OH, -NH 2 , -NO 2 , -CN, -CF 3 , or -OCF 3 .
  • Each R A is independently a C 1-8 aliphatic group, a cycloaliphatic, a heterocycloaliphatic, an aryl, or a heteroaryl, each of which is optionally substituted with 1, 2, or 3 of R D .
  • Each R D is -Z D R 9 , wherein each Z D is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z D are optionally and independently replaced by -CO-, -CS-, -C0NR E -, -C0NR E NR E -, -CO 2 -, -OCO-, -NR E CO 2 -, -0-, -NR E CONR E -, -OCONR E -, -NR E NR E -, -NR B C0-, -S-, -SO-, -SO 2 -, -NR B -, - S0 2 NR E -, -NR E S0 2 -, or -NR E S0 2 NR E -.
  • Each R 9 is independently R E , halo, -OH, -NH 2 , -NO 2 , - CN, -CF 3 , or -OCF 3 .
  • Each R E is independently hydrogen, an optionally substituted C 1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • each R D is independently -Z 0 R 9 ; wherein each Z D can independently be a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z D are optionally and independently replaced by -O-, - NHC(O)-, -C(0)NR E -, -SO 2 -, -NHSO 2 -, -NHC(O)-, -NR E SO 2 -, -SO 2 NH-, -SO 2 NR E -, -NH-, or - C(O)O-.
  • one carbon unit of Z D is replaced by -0-. Or, by -NHC(O)-.
  • R 9 is hydrogen. In some embodiments, R 9 is independently an optionally substituted aliphatic. In some embodiments, R 9 is an optionally substituted cycloaliphatic. Or, is an optionally substituted heterocycloaliphatic. Or, is an optionally substituted aryl. Or, is an optionally substituted heteroaryl. Or, halo.
  • one R 1 is aryl or heteroaryl, each optionally substituted with 1, 2, or 3 of R D , wherein R D is defined above.
  • one R 1 is carboxy [e.g., hydroxycarbonyl or alkoxycarbonyl]. Or, one R 1 is amido [e.g., aminocarbonyl]. Or, one R 1 is amino. Or, is halo. P> if"" T / J 11C f
  • one R 1 that is attached to 5- or 6- position of the pyridyl ring is aryl or heteroaryl, each optionally substituted with 1, 2, or 3 of R D , wherein R D is defined above.
  • the one R 1 attached to the 5- or 6- postion of the pyridyl ring is phenyl optionally substituted with 1, 2, or 3 of R D , wherein R D is defined above.
  • the one Ri attached to the 5- or 6- position of the pyridyl ring is heteroaryl optionally substituted with 1, 2, or 3 of R D .
  • the one Ri attached to the 5- or 6- position of the pyridyl ring is 5 or 6 membered heteroaryl having 1, 2, or 3 heteroatom independently selected from the group consisting of oxygen, nitrogen and sulfur.
  • the 5 or 6 membered heteroaryl is substituted with 1 R D .
  • one Ri attached to the 5- or 6- position of the pyridyl ring is a phenyl substituted with 1 R D .
  • one R 1 attached to the 5- or 6- position of the pyridyl ring is a phenyl substituted with 2 R D .
  • one Ri attached to the 5- or 6- position of the pyridyl ring is a phenyl substituted with 3 R D .
  • R 1 is:
  • Wi is -C(O)-, -SO 2 -, or -CH 2 -;
  • R D is H, hydroxyl, or an optionally substituted group selected from aliphatic, cycloaliphatic, alkoxy, and amino; and R D is defined above.
  • W 1 is -C(O)-.
  • W] is -SO 2 -.
  • Wi is -CH 2 -.
  • D is OH.
  • D is an optionally substituted Ci -6 aliphatic or an optionally substituted C 3 -C 8 cycloaliphatic.
  • D is an optionally substituted alkoxy.
  • D is an optionally substituted amino.
  • D is P £.:: 1 V J U B and B is independently H, an optionally substituted C 1-6 aliphatic, an optionally substituted C 3 -C 8 cycloaliphatic, or
  • a and B taken together, form an optionally substituted 3-7 membered heter ⁇ cycloaliphatic ring.
  • A is H and B is an optionally substituted Ci -6 aliphatic.
  • B is substituted with 1, 2, or 3 substituents. Or, both, A and B, are H.
  • Exemplary substituents include oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, dialkyamino, or an optionally substituted group selected from cycloaliphatic, heterocycloaliphatic, aryl, and heteroaryl.
  • A is H and B is an optionally substituted C 1-6 aliphatic. Or, both, A and B, are H.
  • Exemplary substituents include oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, and an optionally substituted heterocycloaliphatic.
  • B is C 1-6 alkyl, optionally substituted with oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, or an optionally substituted group selected from cycloaliphatic, heterocycloaliphatic, aryl, and heteroaryl.
  • B is substituted with oxo, Ci -6 alkyl, hydroxy, hydroxy-(C 1- e)alkyl, (C 1-6 )alkoxy, (C 1- ⁇ aIkOXy(C 1- 6 )alkyl, C 3 _ 8 cycloaliphatic, 3-8 membered heterocycloaliphatic, phenyl, and 5-10 membered heteroaryl.
  • B is Ci -6 alkyl substituted with optionally substituted phenyl.
  • a and B taken together, form an optionally substituted 3-7 membered heterocycloaliphatic ring.
  • the heterocycloaliphatic ring is optionally substituted with 1, 2, or 3 substituents.
  • Exemplary such rings include optionally substituted pyrrolidinyl, piperidinyl, morpholinyl, and piperazinyl.
  • Exemplary substituents on such rings include halo, oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, acyl (e.g., alkylcarbonyl), amino, amido, and carboxy.
  • the substituent is halo, oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, amino, amido, or carboxy.
  • R D is hydrogen, halo, or an optionally substituted group selected from aliphatic, cycloaliphatic, amino, hydroxy, alkoxy, carboxy, amido, carbonyl, cyano, aryl, or heteroaryl.
  • R D is hydrogen, halo, an optionally substituted Ci -6 aliphatic, or an optionally substituted alkoxy.
  • R D is hydrogen, F, Cl, an optionally substituted Ci -6 alkyl, or an optionally substituted -0(Ci -6 alkyl).
  • R D examples include hydrogen, F, Cl, methyl, ethyl, /-propyl, ⁇ -butyl, -OMe, -OEt, i- propoxy, t-butoxy, CF 3 , or -OCF 3 .
  • R D is hydrogen, F, methyl, methoxy, CF 3 , P C T ./ " Ii S Q IEL/" s+3 F? H cj n n D or -OCF 3 .
  • R can be hydrogen.
  • R can be F.
  • R u can be methyl.
  • R can be methoxy.
  • R 1 is:
  • W 1 is -C(O)-, -SO 2 -, or -CH 2 -;
  • Each of A and B is independently H, an optionally substituted C 1-6 aliphatic, an optionally substituted C 3 -C 8 cycloaliphatic; or
  • a and B taken together, form an optionally substituted 3-7 membered heterocycloaliphatic ring.
  • one R 1 that is attached to the 5- or 6- position of the pyridyl ring is cycloaliphatic or heterocycloaliphatic, each optionally substituted with 1, 2, or 3 of R D ; wherein R D is -Z 0 R 9 ; wherein each Z D is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z are optionally and independently replaced by -CO-, -CS-, -C0NR E -, -C0NR E NR E -, -CO 2 -, -OCO-, -NR E C0 2 -, -O-, -NR E CONR E -, -0C0NR E -, -NR E NR E -, -NR E CO-, -S-, -SO-, -SO 2 -, -NR E -, - SO 2 NR 1 S -NR 13 SO 2 ;
  • one R 1 that is attached to the 5- or 6- position of the pyridyl ring is an optionally substituted C 3 -C 8 cycloaliphatic.
  • one R 1 that is attached to the 5- or 6- position of the pyridyl ring is an optionally substituted C 3 -C 8 cycloalkyl or an optionally substituted C 3 -C 8 cycloalkenyl.
  • one R 1 that is attached to the 5- or 6- position of the pyridyl ring is C 3 -C 8 cycloalkyl or C 3 -C 8 cycloalkenyl.
  • cycloalkyl and cycloalkenyl include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclopentenyl,cyclohexenyl,and cycloheptenyl.
  • Rl is:
  • R 1 is one selected from:
  • Each R 2 can be hydrogen.
  • Each R 2 can be an optionally substituted group selected from C 1-6 aliphatic, C 3-6 cycloaliphatic, phenyl, and heteroaryl.
  • R 2 is a C 1-6 aliphatic optionally substituted with
  • R 2 can be substituted methyl, ethyl, propyl, or butyl. In several examples, R 2 can be methyl, ethyl, propyl, or butyl.
  • R 2 is hydrogen
  • Each R 3 and R' 3 together -with the carbon atom to which they are attached form a C 3 ./ 7 cycloaliphatic or a heterocycloaliphatic, each of which is optionally substituted with 1, 2, or 3 substituents.
  • R 3 and R' 3 together with the carbon atom to which they are attached form a C 3-7 cycloaliphatic or a C 3-7 heterocycloaliphatic, each of which is optionally substituted with 1, 2, or 3 of -Z B R 7 , wherein each Z B is independently a bond, or an optionally substituted branched or straight C 1-4 aliphatic chain wherein up to two carbon units of Z B are optionally and independently replaced by -CO-, -CS-, -CONR B -, -CONR B NR B -, -CO 2 -, - OCO-, -NR 13 CO 2 -, -O-, -NR B CONR B -, -OCONR 5 -, -NR B NR B -, -NR 8 CO-, -S-, -SO-, -SO 2 -, - NR B -, -SO 2 NR B -, -NR B SO 2 ,
  • R 3 and R' 3 together with the carbon atom to which they are attached form a 3, 4, 5, or 6 membered cycloaliphatic that is optionally substituted with 1, 2, or 3 substituents.
  • R 3 , R 3 , and the carbon atom to which they are attached form an optionally substituted cyclopropyl group.
  • R 3 , R' 3 , and the carbon atom to which they are attached form an optionally substituted cyclobutyl group.
  • R 3 , R' 3 , and the carbon atom to which they are attached form an optionally substituted cyclopentyl group.
  • R 3 , R' 3 , and the carbon atom to which they are attached form an optionally substituted cyclohexyl group.
  • R 3 and R 3 together with the carbon atom to which they are attached form an unsubstituted cyclopropyl.
  • R 3 and R 3 together with the carbon atom to which they are attached form a 5, 6, or 7 membered optionally substituted heterocycloaliphatic.
  • R 3 , R' 3 , and the carbon atom to which they are attached form an optionally substituted tetrahydropyranyl group.
  • R 3 and R' 3 together with the carbon atom to which they are attached form an unsubstituted C 3-7 cycloaliphatic or an unsubstituted heterocycloaliphatic.
  • R 3 and R 3 together with the carbon atom to which they are attached form an unsubstituted cyclopropyl, an unsubstituted cyclopentyl, or an unsubstituted cyclohexyl.
  • Each R 4 is independently an optionally substituted aryl or an optionally substituted heteroaryl.
  • R 4 is an aryl having 6 to 10 members (e.g., 7 to
  • R 4 10 members optionally substituted with 1, 2, or 3 substituents.
  • R 4 include optionally substituted benzene, naphthalene, or indene.
  • examples of R 4 can be optionally substituted phenyl, optionally substituted naphthyl, or optionally substituted indenyl.
  • R 4 is an optionally substituted heteroaryl.
  • R 4 examples include monocyclic and bicyclic heteroaryl, such a benzofused ring system in which the phenyl is fused with one or two 4-8 membered heterocycloaliphatic groups.
  • R 4 is an aryl or heteroaryl, each optionally substituted with 1, 2, or 3 of -Z 0 R 8 .
  • R 4 is an aryl optionally substituted with 1, 2, or 3 of -Z 0 R 8 .
  • R 4 is phenyl optionally substituted with 1, 2, or 3 of -Z 0 R 8 .
  • R 4 is a heteroaryl optionally substituted with 1, 2, or 3 of -Z 0 R 8 .
  • Each Z° is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z° are optionally and independently replaced by -CO-, -CS-, - CONR 0 -, -CONR 0 NR 0 -, -CO 2 -, -OCO-, -NR 0 CO 2 -, -O-, -NR 0 CONR 0 -, -OCONR 0 -, -NR 0 NR 0 - , -NR 0 CO-, -S-, -SO-, -SO 2 -, -NR 0 -, -SO 2 NR 0 -, -NR 0 SO 2 -, or -NR 0 SO 2 NR 0 -.
  • Each R 8 is independently R c , halo, -OH, -NH 2 , -NO 2 , -CN, -CF 3 , or -OCF 3 .
  • Each R c is independently hydrogen, an optionally substituted C 1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • two occurrences of -Z 0 R 8 taken together with carbons to which they are attached, form a 4-8 membered saturated, partially saturated, or aromatic ring with up to 3 ring atoms independently selected from the group consisting of O, NH, NR C , and S; wherein R c is defined herein.
  • R 4 is one selected from
  • R 1 is an optionally substituted cyclic group that is attached to the core structure at the 5 or 6 position of the pyridine ring.
  • Ri is an optionally substituted aryl that is attached to the 5 position of the pyridine ring.
  • R 1 is an optionally substituted aryl that is attached to the 6 position of the pyridine ring.
  • Rj is an optionally substituted heteroaryl that is attached to the 5 position of the pyridine ring.
  • R 1 is an optionally substituted heteroaryl that is attached to the 6 position of the pyridine ring.
  • R 1 is an optionally substituted cycloaliphatic or an optionally substituted heterocycloaliphatic that is attached to the pyridine ring at the 5 or 6 position.
  • each R 1 is aryl or heteroaryl optionally substituted with 1, 2, or 3 of R D , wherein R D is -Z 0 Rg, wherein each Z D is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z D are optionally and independently replaced by -CO-, -CS-, -CONR E -, -CONR E NR E -, -CO 2 -, - OCO-, -NR E CO 2 -, -O-, -NR E CONR E -, -OCONR E -, -NR E NR E -, -NR E CO-, -S-, -SO-, -SO 2 -, - NR E -, -SO 2 NR E -, -NR E SO 2 -, or -NR E SO 2 NR E -; each R 9 is independently R E , halo,
  • each R 1 is cycloaliphatic or heterocycloaliphatic optionally substituted with 1, 2, or 3 of R D ; wherein R D is defined above.
  • Another aspect of the present invention provides compounds of formula
  • each R 1 is aryl or heteroaryl optionally substituted with 1, 2, or 3 of R D , wherein R D is -Z 0 Rg, wherein each Z D is independently a bond or an optionally substituted branched or straight Ci -6 aliphatic chain wherein up to two carbon units of Z D are optionally and independently replaced by -CO-, -CS-, -CONR E -, -C0NR E NR E -, -CO 2 -, - OCO-, -NR E CO 2 -, -O-, -NR E C0NR E -, -OCONR E -, -NR E NR E -, -NR E C0-, -S-, -SO-, -SO 2 -, - NR E -, -SO 2 NR E -, -NR E SO 2 -, or -NR E SO 2 NR E -; each R 9 is independently R E ,
  • each R 1 is cycloaliphatic or heterocycloaliphatic optionally substituted with 1, 2, or 3 of R D ; wherein R D is defined above.
  • the present invention includes compounds of formula
  • R D is -Z 0 R 9 ; wherein each Z D is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z D are optionally and independently replaced by -CO-, -CS-, -CONR E -, -CONR E NR E -, -CO 2 -, -OCO-, -NR E C0 2 -, -O-, -NR E CONR E -, -OCONR E -, -NR E NR E -, -NR E CO-, -S-, -SO-, -SO 2 -, -NR E -, - SO 2 NR E -, -NR E SO 2 -, or -NR E S0 2 NR E -.
  • R 9 is independently R E , halo, -OH, -NH 2 , -NO 2 , -CN, -CF 3 , or -OCF 3 .
  • Each R E is independently hydrogen, an optionally substituted C 1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • Z D is independently a bond or is an optionally substituted branched or straight C 1-6 aliphatic chain wherein one carbon unit of Z D is optionally replaced by -SO 2 -, -CONR E -, - NR E SO 2 -, or -SO 2 NR E -.
  • Z D is an optionally substituted branched or straight C 1-6 aliphatic chain wherein one carbon unit of Z D is optionally replaced by -SO 2 -.
  • R 9 is an optionally substituted heteroaryl or an optionally substituted heterocycloaliphatic.
  • R 9 is an optionally substituted heterocycloaliphatic having 1-2 nitrogen atoms, and R 9 attaches directly to -SO 2 - via a ring nitrogen.
  • the present invention includes compounds of formula
  • V-A or formula V-B:
  • V-A V-B or a pharmaceutically acceptable salt thereof, wherein:
  • T is an optionally substituted C 1-2 aliphatic chain, wherein each of the carbon units is optionally and independently replaced by -CO-, -CS-, -COCO-, -SO 2 -, -B(OH)-, or -B(O(C 1-6 alkyl))-;
  • Each of Ri' and Ri" is independently a bond or an optionally substituted Ci -6 aliphatic, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted 3 to 10 membered cycloaliphatic, an optionally substituted 3 to 10 membered heterocycloaliphatic, carboxy, amido, amino, halo, or hydroxy;
  • R m is attached to carbon 3" or 4"; each R D1 and R D2 is -Z D R 9 , wherein each Z D is independently a bond or an optionally substituted branched or straight Ci -6 aliphatic chain wherein up to two carbon units of Z D are optionally and independently replaced by -CO-, -CS-, -C0NR E -, -C0NR E NR E -, -CO 2 -, -OCO-, -NR E C0 2 -, -O-, -NR E C0NR E -, -0C0NR E -, -NR E NR E -, -NR E C0-, -S-, -SO-, -SO 2 -, -NR E -, - S0 2 NR E -, -NR E SO 2 -, or -NR E S0 2 NR E -;
  • R 9 is independently R E , halo, -OH, -NH 2 , -NO 2 , -CN, -CF 3 , or -OCF 3 ; or R D1 and R D2 , taken together with atoms to which they are attached, form a 3-8 membered saturated, partially unsaturated, or aromatic ring with up to 3 ring members independently selected from the group consisting of O, NH, NR , and S; and each R E is independently hydrogen, an optionally substituted C 1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
  • T is an optionally substituted -CH 2 -. In some other embodiments, T is an optionally substituted -CH 2 CH 2 -.
  • T is optionally substituted by -Z E R 10 ; wherein each Z E is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z B are optionally and independently replaced by -CO-, - CS-, -CONR F -, -CONR F NR F -, -CO 2 -, -OCO-, -NR F CO 2 -, -O-, -NR F CONR F -, -OCONR F -, - NR F NR F -, -NR F CO-, -S-, -SO-, -SO 2 -, -NR F -, -SO 2 NR F -, -NR F SO 2 -, or -NR F SO 2 NR F -;
  • R 10 is independently R F , halo, -OH, -NH 2 , -NO 2 , -CN, -
  • R 1 Q can be an optionally substituted C 1-6 alkyl, an optionally substituted C 2-6 alkenyl, an optionally substituted C 3-7 cycloaliphatic, or an optionally substituted C 6-10 aryl.
  • R 1O is methyl, ethyl, /-propyl, or /-butyl.
  • up to two carbon units of T are optionally substituted by -CO-, -CS-, -B(OH)-, or -B(O(Ci -6 alkyl)-.
  • T is selected from the group consisting of -CH 2 -, -
  • T is -C(CH 3 ) 2 -.
  • each of R 1 ' and R 1 " is hydrogen.
  • each Of R 1 ' and R 1 " is independently -Z A Rs, wherein each Z A is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z A are optionally and independently replaced by -CO-, -CS-, -CONR A -, - CONR A NR A -, -CO 2 -, -OCO-, -NR A C0 2 -, -0-, -NR A C0NR A -, -0C0NR A -, -NR A NR A -, - NR A CO-, -S-, -SO-, -SO 2 -, -NR A -, -SO 2 NR A -, -NR A S0 2 -, or -NR A SO 2 NR A -.
  • Each R 5 is independently R A , halo, -OH, -NH 2 , -NO 2 , -CN, -CF 3 , or -OCF 3 .
  • Each R A is independently an optionally substituted group selected from C 1-8 aliphatic group, a cycloaliphatic, a heterocycloaliphatic, an aryl, and a heteroaryl.
  • R 1 ' is selected from the group consisting of H, C 1-6 aliphatic, halo, CF 3 , CHF 2 , -0(C 1-6 aliphatic), C3-C5 cycloalkyl, or C4-C6 heterocycloalkyl containing one oxygen atom.
  • R 1 ' is selected from the group consisting of H, methyl, ethyl, i-propyl, t-butyl, F. Cl, CF 3 , CHF 2 , -OCH 3 , -OCH 2 CH 3 , -O-(z-propyl), or -O- (t-butyl). More preferably, R 1 1 Is H. Or, R 1 ' is methyl. Or, ethyl. Or 5 CF 3 .
  • R 1 " is selected from the group consisting of H, C 1-
  • R 1 " is selected from the group consisting of H 5 methyl, ethyl, z-propyl, t-butyl, F. Cl, CF 3 , CHF 2 , -OCH 3 , - OCH 2 CH 3 , -O-( ⁇ -propyl), or -O-(t-butyl). More preferably, R 1 " is H. Or, R 1 " is methyl. Or, ethyl. Or 5 CF 3 .
  • R m is attached to carbon 3" or 4", and is -Z D R 9 , wherein each Z D is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein up to two carbon units of Z D are optionally and independently replaced by -CO-, -CS-, -C0NR E -, -CONR E NR E -, -CO 2 -, -OCO-, -NR 2 CO 2 -, -O-, -NR E C0NR E -, - 0C0NR E - 5 -NR E NR E -, -NR E C0-, -S-, -SO-, -SO 2 -, -NR E - 5 -SO 2 NR E - 5 -NR E SO 2 - 5 or - NR E S ⁇ 2 NR E -.
  • Z D is independently a bond or an optionally substituted branched or straight C 1-6 aliphatic chain wherein one carbon unit of Z D is optionally replaced by -CO-, -SO-, -SO 2 -, -COO-, -OCO-, -CONR E -, -NR E C0-, NR E C0 2 -, -0-, -NR 12 SO 2 - , or -S ⁇ 2NR E -.
  • one carbon unit of Z D is optionally replaced by -CO-. Or, by -SO-. Or, by -SO 2 -. Or, by -COO-. Or, by -OCO-. Or 5 by -C0NR E -. Or, by -NR E CO-. Or, by -NR E C0 2 -. Or, by -O-. Or, by -NR E SO 2 -. Or, by -SO 2 NR E -.
  • R 9 is hydrogen, halo, -OH, -NH 2 , -CN, -CF 3 , -
  • R 9 is hydrogen, F, Cl, -OH, -CN, -CF 3 , or -OCF 3 .
  • R 9 is C 1-6 aliphatic, C 3-8 cycloaliphatic, 3-8 membered heterocycloaliphatic, Cg-io aryl, and 5-10 membered heteroaryl, each of which is optionally substituted by 1 or 2 substituents independently selected from the group consisting of R E , oxo, halo, -OH, -NR E R B , -OR E , - COOR E , and -CONR E R E .
  • R 9 is optionally substituted by 1 or 2 substituents independently selected from the group consisting of oxo, F, Cl, methyl, ethyl, i- propyl, ⁇ -butyl, -CH 2 OH, -CH 2 CH 2 OH, -C(O)OH, -C(O)NH 2 , -CH 2 O(Ci -6 alkyl), - CH 2 CH 2 O(C 1-6 alkyl), and -C(O)(Ci -6 alkyl).
  • R 9 is hydrogen.
  • R 9 is selected from the group consisting of Ci -6 straight or branched alkyl or C 2- ( S straight or branched alkenyl; wherein said alkyl or alkenyl is optionally substituted by 1 or 2 substituents independently selected from the group consisting of R E , oxo, halo, -OH, -NR E R E , -0R E , - COOR E , and -CONR E R E .
  • R 9 is C 3-8 cycloaliphatic optionally substituted by
  • cycloaliphatic examples include but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl.
  • R 9 is a 3-8 membered heterocyclic with 1 or 2 heteroatoms independently selected from the group consisting of O, NH, NR E , and S; wherein said heterocyclic is optionally substituted by 1 or 2 substituents independently selected from the group R E , oxo, halo, -OH, -NR E R E , -0R E , -COOR E , and -CONR E R E .
  • Example of 3-8 membered heterocyclic include but are not limited to
  • R 9 is an optionally substituted 5-8 membered heteroaryl with one or two ring atom independently selected from the group consisting of O, S, and NR E .
  • 5-8 membered heteroaryl include but are not limited to
  • R DI and R D2 taken together with carbons to which they are attached, form an optionally substituted 4-8 mer ⁇ bered saturated, partially unsaturated, or aromatic ring with 0-2 ring atoms independently selected from the group consisting of O, NH, NR E , and S.
  • R DI and R D2 taken together with phenyl containing carbon atoms 3" and 4", include but are not limited to
  • R D2 is selected from the group consisting of H, R E , halo, -OH, -(CH 2 ) r NR E R E , -(CH 2 ) r -OR E , -SO 2 -R E , -NR E -SO 2 ⁇ R E , -SO 2 NR E R E , -C(O)R E , - C(O)OR E , -OC(O)OR E , -NR E C(O)OR E ? and -C(O)NR E R E ; wherein r is 0, 1, or 2.
  • R m is selected from the group consisting of H, Ci -6 aliphatic, halo, -CN, -NH 2 , - NH(C 1-6 aliphatic), -N(Ci -6 aliphatic) 2 , -CH 2 -N( C 1-6 aliphatic) 2 , -CH 2 -NH(C 1-6 aliphatic), - CH 2 NH 2 , -OH, -0(Ci -6 aliphatic), -CH 2 OH, -CH 2 -O(Ci -6 aliphatic), -SO 2 ( C 1-6 aliphatic), -N( C 1-6 aliphatic)-SO 2 (C V 6 aliphatic), -NH-SO 2 (C 1-6 aliphatic), -SO 2 NH 2 , -SO 2 NH(Ci -6 aliphatic), - SO 2 N( C 1-6 aliphatic) 2 , -C(O)(
  • R D2 is selected from the group consisting of H, Ci -6 aliphatic, halo, -CN, -NH 2 , -CH 2 NH 2 , -OH, -0(Ci -6 aliphatic), - CH 2 OH, -SO 2 ( C 1-6 aliphatic), -NH-SO 2 (C 1-6 aliphatic), -C(O)O(Ci -6 aliphatic), -C(O)OH, - NHC(O)(C 1-6 aliphatic), -C(O)NH 2 , -C(O)NH(C 1-6 aliphatic), and -C(O)N(C 1-6 aliphatic) 2 .
  • R D2 is selected from the group consisting of H, methyl, ethyl, n-propyl, i-propyl, t- butyl, F, Cl, CN, -NH 2 , -CH 2 NH 2 , -OH, -OCH 3 , -O-ethyl, -O-(i-propyl), -O ⁇ (n-propyl), - CH 2 OH, -SO 2 CH 3 , -NH-SO 2 CH 3 , -C(O)OCH 3 , -C(O)OCH 2 CH 3 , -C(O)OH, -NHC(O)CH 3 , - C(O)NH 2 , and -C(O)N(CHs) 2 .
  • R D2 is hydrogen.
  • R D2 is hydrogen.
  • the present invention provides compounds of formula VI-A -i or formula VI-A-ii:
  • T, R m , R m , and R 1 ' are as defined above.
  • T is -CH 2 -, -CF 2 -, or -C(CH 3 ) 2 -.
  • Ri' is selected from the group consisting of H, C 1-6 aliphatic, halo, CF 3 , CHF 2 , -0(Cj -5 aliphatic), C3-C5 cycloalkyl, or C4-C6 heterocycloalkyl containing one oxygen atom.
  • Exemplary embodiments include H, methyl, ethyl, i-propyl, t- butyl, F. Cl, CF 3 , CHF 2 , -OCH 3 , -OCH 2 CH 3 , -O-(i- ⁇ ropyl), -O-(t-butyl), cyclopropyl, or oxetanyl. More preferably, R 1 ' is H. Or, R 1 ' is methyl. Or, ethyl. Or, CF 3 . Or, oxetanyl.
  • R m is Z D R 9 , wherein Z D is selected from CONH,
  • R m is Z D R 9 , wherein Z D is selected from CONH, SO 2 NH, SO 2 N(C 1-6 alkyl), CH 2 NHSO 2 , CH 2 N(CH 3 )SO 2 , CH 2 NHCO, COO, SO 2 , or CO.
  • Z D is COO and R 9 is H.
  • 2? is
  • COO and R 9 is an optionally substituted straight or branched C 1-6 aliphatic.
  • Z D is COO and R 9 is an optionally substituted straight or branched Ci- ⁇ alkyl.
  • Z D is COO and R 9 is C 1-6 alkyl.
  • Z D is COO and R 9 is methyl.
  • Z D is CONH and R 9 is H. In one embodiment, Z D is
  • CONH and R 9 is an optionally substituted straight or branched C 1-6 aliphatic.
  • Z D is CONH and R 9 is straight or branched C 1-6 alkyl.
  • Z D is CONH and R 9 is methyl.
  • Z D is CONH and R 9 is an optionally substituted straight or branched C 1-6 alkyl.
  • Z D is CONH and R 9 is 2-(dimethylamino)-ethyl.
  • Z D is CH 2 NHCO and R 9 is an optionally substituted straight or branched C 1-6 aliphatic or an optionally substituted alkoxy.
  • Z D is CH 2 NHCO and R 9 is straight or branched C 1-6 alkyl optionally substituted with halo, oxo, hydroxyl, or an optionally substituted group selected from aliphatic, cyclic, aryl, heteroaryl, alkoxy, amino, carboxyl, or carbonyl.
  • Z D is CH 2 NHCO and R 9 is methyl.
  • Z D is CH 2 NHCO and R 9 is CF 3 .
  • Z D is CH 2 NHCO and R 9 is t-butoxy.
  • Z D is SO 2 NH and R 9 is H.
  • Z D is SO 2 NH and R 9 is an optionally substituted straight or branched C 1-6 aliphatic.
  • Z D is SO 2 NH and R 9 is is straight or branched Ci -6 alkyl optionally substituted with halo, oxo, hydroxyl, or an optionally substituted group selected from C 1-6 aliphatic, 3-8 membered cyclic, C 6-1O aryl, 5-8 membered heteroaryl, alkoxy, amino, amido, carboxyl, or carbonyl.
  • Z D is SO 2 NH and R 9 is methyl.
  • Z D is SO 2 NH and R 9 is ethyl. In one embodiment, Z D is SO 2 NH and R 9 is /-propyl. In one embodiment, Z D is SO 2 NH and R 9 is t-butyl. In one embodiment, Z D is SO 2 NH and R 9 is 3,3- dimethylbutyl. In one embodiment, Z D is SO 2 NH and R 9 is CH 2 CH 2 OH. In one embodiment, Z D is SO 2 NH and R 9 is CH(CH 3 )CH 2 OH. In one embodiment, Z D is SO 2 NH and R 9 is CH 2 CH(CH 3 )OH. In one embodiment, Z D is SO 2 NH and R 9 is CH(CH 3 )OH. In one embodiment, Z D is SO 2 NH and R 9 is CH(CH 2 OH) 2 .
  • Z D is SO 2 NH and R 9 is CH 2 CH(OH)CH 2 OH. In one embodiment, Z D is SO 2 NH and R 9 is CH 2 CH(OH)CH 2 CH 3 . In one embodiment, Z D is SO 2 NH and R 9 is C(CH 3 ) 2 CH 2 OH. In one embodiment, Z D is SO 2 NH and R 9 is CH(CH 2 CH 3 )CH 2 OH. In one embodiment, Z D is SO 2 NH and R 9 is CH 2 CH 2 OCH 2 CH 2 OH. In one embodiment, Z D is SO 2 NH and R 9 is C(CH 3 )(CH 2 OH) 2 .
  • Z D is SO 2 NH and R 9 is CH 2 CH(OH)CH 2 C(O)OH. In one embodiment, Z D is SO 2 NH and R 9 is CH 2 CH 2 N(CH 3 ) 2 . In one embodiment, Z D is SO 2 NH and R 9 is CH 2 CH 2 NHC(O)CH 3 . In one embodiment, Z D is SO 2 NH and R 9 is CH(CH(CH 3 ) 2 )CH 2 OH. In one embodiment, Z D is SO 2 NH and R 9 is CH(CH 2 CH 2 CH 3 )CH 2 OH. In one embodiment, Z D is SO 2 NH and R 9 is 1-tetrahydrofuryl-methyl. In one embodiment, Z is SO 2 NH and R 9 is furylmethyl.
  • Z D is SO 2 NH and R 9 is (5-methylfuryl)- methyl. In one embodiment, Z D is SO 2 NH and R 9 is 2-pyrrolidinylethyl. In one embodiment, Z D is SO 2 NH and R 9 is 2-(l-methylpyrrolidinyl)-ethyl. In one embodiment, Z D is SO 2 NH and R 9 is 2-(4-morpholinyl)-ethyl. In one embodiment, Z D is SO 2 NH and R 9 is 3-(4-morpholinyl)- propyl. In one embodiment, Z D is SO 2 NH and R 9 is C(CH 2 CH 3 )(CH 2 OH) 2 .
  • Z D is SO 2 NH and R 9 is 2-(lH-imidazol ⁇ 4-yl)ethyl. In one embodiment, Z D is SO 2 NH and R 9 is 3-(lH-imidazol-l-yl) ⁇ propyl. In one embodiment, Z D is SO 2 NH and R 9 is 2- (2-pyridinyl)-ethyl.
  • Z D is SO 2 NH and R 9 is an optionally substituted
  • Z D is SO 2 NH and R 9 is an optionally substituted C 1-6 cycloalkyl. In several examples, Z D is SO 2 NH and R 9 is C 1-6 cycloalkyl. In one embodiment, Z D is SO 2 NH and R 9 is cyclobutyl. In one embodiment, Z D is SO 2 NH and R 9 is cyclopentyl. In one embodiment, Z D is SO 2 NH and R 9 is cyclohexyl.
  • Z D is SO 2 N(C 1-6 alkyl) and R 9 is an optionally substituted straight or branched C 1-6 aliphatic or an optionally substituted cycloaliphatic.
  • Z D is SO 2 N(C 1-6 alkyl) and R 9 is an optionally substituted straight or branched Ci -6 aliphatic.
  • Z D is SO 2 N(Ci -6 alkyl) and R 9 is an optionally substituted straight or branched C 1-6 alkyl or an optionally substituted straight or branched C 1-6 alkenyl.
  • Z D is SO 2 N(CH 3 ) and R 9 is methyl.
  • Z D is SO 2 N(CH 3 ) and R 9 is n-propyl. In one embodiments, Z D is SO 2 N(CH 3 ) and R 9 is n-butyl. In one embodiments, Z D is SO 2 N(CH 3 ) and R 9 is cyclohexyl. In one embodiments, Z D is SO 2 N(CH 3 ) and R 9 is allyl. In one embodiments, Z D is SO 2 N(CH 3 ) and R 9 is CH 2 CH 2 OH. In one embodiments, Z D is SO 2 N(CH 3 ) and R 9 is CH 2 CH(OH)CH 2 OH. In one embodiments, Z D is SO 2 N(CH 2 CH 2 CH 3 ) and R 9 is cyclopropylmethyl.
  • Z D is CH 2 NHSO 2 and R 9 is methyl. In one embodiment, Z D is CH 2 N(CH 3 )SO 2 and R 9 is methyl.
  • Z D is SO 2 and R 9 is an optionally substituted C 1-6 straight or branched aliphatic or an optionally substituted 3-8 membered heterocyclic, having 1, 2, or 3 ring members selected from the group consisting of nitrogen, oxygen, sulfur, SO, or SO2.
  • Z D is SO 2 and R 9 is straight or branched Ci -6 alkyl or 3-8 membered heterocycloaliphatic each of which is optionally substituted with 1, 2, or 3 of oxo, halo, hydroxyl, or an optionally substituted group selected from Ci -6 aliphatic, carbonyl, amino, and carboxy.
  • Z D is SO 2 and R 9 is methyl.
  • Z is SO 2 and examples of R 9 include
  • R D2 is H, hydroxyl, halo, C 1-6 alkyl, C 1-6 alkoxy,
  • R D2 is H, halo, C 1-4 alkyl, or C 1-4 alkoxy.
  • R D2 include H, F, Cl, methyl, ethyl, and methoxy.
  • the present invention provides compounds of formula (I'-A) or formula (I'-B):
  • R 1 , R 2 , R 3 , R' 3 , R 4 , and n are defined above.
  • R 1 is an optionally substituted aryl.
  • R 1 is phenyl optionally substituted with 1, 2, or 3 of halo, OH, -0( C 1-6 aliphatic), amino, C 1-6 aliphatic, C 3-7 cycloaliphatic, 3-8 membered heterocycloaliphatic, C 6-10 aryl, or 5-8 membered heteroaryl.
  • Ri is phenyl optionally substituted with alkoxy, halo, or amino.
  • R 1 is phenyl.
  • R 1 is phenyl substituted with Cl, methoxy, ethoxy, or dimethylamino.
  • R 2 is hydrogen. In some embodiments, R 2 is optionally substituted C 1-6 aliphatic.
  • R 3 , R' 3 , and the carbon atom to which they are attached form an optionally substituted C 3-8 cycloaliphatic or an optionally substituted 3-8 membered heterocycloaliphatic. In some embodiments, R 3 , R 3 , and the carbon atom to which they are attached form an optionally substituted C 3-8 cycloalkyl. In one example, R 3 , R' 3 , and the carbon atom to which they are attached is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl or cycloheptyl, each of which is optionally substituted.
  • R 3 , R' 3 , and the carbon atom to which they are attached is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl or cycloheptyl.
  • R3, R' 3 , and the carbon atom to which they are attached is cyclopropyl.
  • R 4 is an optionally substituted aryl or an optionally substituted heteroaryl. In some embodiments, R 4 is an optionally substituted phenyl. In several embodiments, R 4 is phenyl fused to a 3, 4, 5, or 6 membered heterocyclic having 1, 2, or 3 ring membered selected from oxygen, sulfur and nitrogen. In several embodiments, R 4 is
  • T is defined above.
  • T is -CH 2 -.
  • Exemplary compounds of the present invention include, but are not limited to, those illustrated in Table 1 below. [00307] Table 1 : Examples of compounds of the present invention
  • a nitrite of formula i is alkylated (step a) with a dihalo-aliphatic in the presence of abase such as, for example, 50% sodium hydroxide and, optionally, a phase transfer reagent such as, for example, benzyltriethylammonium chloride (BTEAC), to produce the corresponding alkylated nitrile (not shown) which on hydrolysis produces the acid ii.
  • BTEAC benzyltriethylammonium chloride
  • Compounds of formula ii are converted to the acid chloride iii with a suitable reagent such as, for example, thionyl chloride/DMF.
  • step c Reaction of the acid chloride iii with an aminopyridine, wherein X is a halo, of formula iv (step c) produces the amide of formula v.
  • step d Reaction of the amide v with an optionally substituted boronic acid derivative (step d) in the presence of a catalyst such as, for example, palladium acetate or dichloro-[l,l- bis(di ⁇ henylphosphino) ferrocene] palladium(H) (Pd(dppf)Cl 2 ) , provides compounds of the invention wherein R 1 is aryl, heteroaryl, or cycloalkenyl.
  • a catalyst such as, for example, palladium acetate or dichloro-[l,l- bis(di ⁇ henylphosphino) ferrocene] palladium(H) (Pd(dppf)Cl 2 )
  • the boronic acid derivatives vi are commercially available or may be prepared by known methods such as reaction of an aryl bromide with a diborane ester in the presence of a coupling reagent such as, for example, palladium acetate as described in the examples.
  • a coupling reagent such as, for example, palladium acetate as described in the examples.
  • X is halo and Q is C 1-6 aliphatic, aryl, heteroaryl, or 3 to 10 membered cycloaliphatic or heterocycloaliphatic as a substitute for the aminopyridine of formula iv.
  • compositions comprising any of the compounds as described herein, and optionally comprise a pharmaceutically acceptable carrier, adjuvant or vehicle.
  • these compositions optionally further comprise one or more additional therapeutic agents.
  • a pharmaceutically acceptable derivative or a prodrug includes, but is not limited to, pharmaceutically acceptable salts, esters, salts of such esters, or any other adduct or derivative which upon administration to a patient in need is capable of providing, directly or indirectly, a compound as otherwise described herein, or a metabolite or residue thereof.
  • the term "pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio.
  • a “pharmaceutically acceptable salt” means any non-toxic salt or salt of an ester of a compound of this invention that, upon administration to a recipient, is capable of providing, either directly or indirectly, a compound of this invention or an inhibitorily active metabolite or residue thereof.
  • Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases.
  • suitable inorganic and organic acids and bases include those derived from suitable inorganic and organic acids and bases.
  • pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange.
  • salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate,
  • Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N + (C 1-4 EIkVl) 4 salts.
  • This invention also envisions the quaternization of any basic nitrogen-containing groups of the compounds disclosed herein. Water or oil-soluble or dispersable products may be obtained by such quaternization.
  • Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like.
  • Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate and aryl sulfonate.
  • compositions of the present invention additionally comprise a pharmaceutically acceptable carrier, adjuvant, or vehicle, which, as used herein, includes any and all solvents, diluents, or other liquid vehicle, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired.
  • a pharmaceutically acceptable carrier, adjuvant, or vehicle which, as used herein, includes any and all solvents, diluents, or other liquid vehicle, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired.
  • Remington The Science and Practice of Pharmacy, 21st edition, 2005, ed. D.B. Troy, Lippincott Williams & Wilkins, Philadelphia, and Encyclopedia of Pharmaceutical Technology, eds. J
  • materials which can serve as pharmaceutically acceptable carriers include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, or potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, wool fat, sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc
  • the present invention provides a method of treating a condition, disease, or disorder implicated by ABC transporter activity.
  • the present invention provides a method of treating a condition, disease, or disorder implicated by a deficiency of ABC transporter activity, the method comprising administering a composition comprising a compound of formulae (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B) to a subject, preferably a mammal, in need thereof.
  • the present invention provides a method of treating Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronernia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay ⁇ Sachs, Crigler-Najjar type ⁇ , Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1, Hereditary emphysema, Congenital hypert
  • the present invention provides a method of treating cystic fibrosis comprising the step of administering to said mammal a composition comprising the step of administering to said mammal an effective amount of a composition comprising a compound of formulae (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B), or a preferred embodiment thereof as set forth above.
  • a composition comprising a compound of formulae (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B), or a preferred embodiment thereof as set forth above.
  • an "effective amount" of the compound or pharmaceutically acceptable composition is that amount effective for treating or lessening the severity of one or more of Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1, Heredit
  • the compounds and compositions, according to the method of the present invention may be administered using any amount and any route of administration effective for treating or lessening the severity of one or more of Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis
  • the exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular agent, its mode of administration, and the like.
  • the compounds of the invention are preferably formulated in dosage unit form for ease of administration and uniformity of dosage.
  • dosage unit form refers to a physically discrete unit of agent appropriate for the patient to be treated. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment.
  • the specific effective dose level for any particular patient or organism will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed, and like factors well known in the medical arts.
  • patient means an animal, preferably a mammal, and most preferably a human.
  • compositions of this invention can be administered to humans and other animals orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, or drops), bucally, as an oral or nasal spray, or the like, depending on the severity of the infection being treated.
  • the compounds of the invention may be administered orally or parenterally at dosage levels of about 0.01 mg/kg to about 50 mg/kg and preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.
  • Liquid dosage forms for oral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs.
  • the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.
  • the oral compositions can also include
  • Injectable preparations for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol.
  • acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S. P. and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
  • a compound of the present invention In order to prolong the effect of a compound of the present invention, it is often desirable to slow the absorption of the compound from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the compound then depends upon its rate of dissolution that, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered compound form is accomplished by dissolving or suspending the compound in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the compound in biodegradable polymers such as polylactide-polyglycolide.
  • the rate of compound release can be controlled.
  • biodegradable polymers include poly(orthoesters) and poly(anhydrides).
  • Depot injectable formulations are also prepared by entrapping the compound in liposomes or microemulsions that are compatible with body tissues.
  • compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
  • suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
  • Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules.
  • the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar— agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cety
  • Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.
  • the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polethylene glycols and the like.
  • the active compounds can also be in microencapsulated form with one or more excipients as noted above.
  • the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art.
  • the active compound may be admixed with at least one inert diluent such as sucrose, lactose or starch.
  • Such dosage forms may also comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose.
  • the dosage forms may also comprise buffering agents. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner.
  • buffering agents include polymeric substances and waxes.
  • Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches.
  • the active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required.
  • Ophthalmic formulation, eardrops, and eye drops are also contemplated as being within the scope of this invention.
  • the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a compound to the body.
  • Such dosage forms are prepared by dissolving or dispensing the compound in the proper medium.
  • Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.
  • the compounds of the invention are useful as modulators of ABC transporters.
  • the compounds and compositions are particularly useful for treating or lessening the severity of a disease, condition, or disorder where hyperactivity or inactivity of ABC transporters is implicated in the disease, condition, or disorder.
  • hyperactivity or inactivity of an ABC transporter is implicated in a particular disease, condition, or disorder
  • the disease, condition, or disorder may also be referred to as an "ABC transporter-mediated disease, condition or disorder”.
  • the present invention provides a method for treating or lessening the severity of a disease, condition, or disorder where hyperactivity or inactivity of an ABC transporter is implicated in the disease state.
  • ABC transporter may be assayed according to methods described generally in the art and in the Examples herein.
  • the compounds and pharmaceutically acceptable compositions of the present invention can be employed in combination therapies, that is, the compounds and pharmaceutically acceptable compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures.
  • the particular combination of therapies (therapeutics or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutics and/or procedures and the desired therapeutic effect to be achieved.
  • the therapies employed may achieve a desired effect for the same disorder (for example, an inventive compound may be administered concurrently with another agent used to treat the same disorder), or they may achieve different effects (e.g., control of any adverse effects).
  • additional therapeutic agents that are normally administered to treat or prevent a particular disease, or condition are known as "appropriate for the disease, or condition, being treated".
  • the amount of additional therapeutic agent present in the compositions of this invention will be no more than the amount that would normally be administered in a composition comprising that therapeutic agent as the only active agent.
  • the amount of additional therapeutic agent in the presently disclosed compositions will range from about 50% to 100% of the amount normally present in a composition comprising that agent as the only therapeutically active agent.
  • the present invention in another aspect, includes a composition for coating an implantable device comprising a compound of the present invention as described generally above, and in classes and subclasses herein, and a carrier suitable for coating said implantable device.
  • the present invention includes an implantable device coated with a composition comprising a compound of the present invention as described generally above, and in classes and subclasses herein, and a carrier suitable for coating said implantable device.
  • Suitable coatings and the general preparation of coated implantable devices are described in US Patents 6,099,562; 5,886,026; and 5,304,121.
  • the coatings are typically biocompatible polymeric materials such as a hydrogel polymer, polymethyldisiloxane, polycaprolactone, polyethylene glycol, polylactic acid, ethylene vinyl acetate, and mixtures thereof.
  • the coatings may optionally be further covered by a suitable topcoat of fluorosilicone, polysaccarides, polyethylene glycol, phospholipids or combinations thereof to impart controlled release characteristics in the composition.
  • Another aspect of the invention relates to modulating ABC transporter activity in a biological sample or a patient (e.g., in vitro or in vivo), which method comprises administering to the patient, or contacting said biological sample with a compound of formula I or a composition comprising said compound.
  • biological sample includes, without limitation, cell cultures or extracts thereof; biopsied material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts thereof.
  • Modulation of ABC transporter activity in a biological sample is useful for a variety of purposes that are known to one of skill in the art. Examples of such purposes include, but are not limited to, the study of ABC transporters in biological and pathological phenomena; and the comparative evaluation of new modulators of ABC transporters.
  • a method of modulating activity of an anion channel in vitro or in vivo comprising the step of contacting said channel with a compound of formulae (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B).
  • the anion channel is a chloride channel or a bicarbonate channel.
  • the anion channel is a chloride channel. I>C T./llSQB /M-35e'g
  • the present invention provides a method of increasing the number of functional ABC transporters in a membrane of a cell, comprising the step of contacting said cell with a compound of formula (I, II, III, IV, V-A, V- B, I', I'-A, and I'-B).
  • functional ABC transporter as used herein means an ABC transporter that is capable of transport activity.
  • said functional ABC transporter is CFTR.
  • the activity of the ABC transporter is measured by measuring the transmembrane voltage potential.
  • Means for measuring the voltage potential across a membrane in the biological sample may employ any of the known methods in the art, such as optical membrane potential assay or other electrophysiological methods.
  • the optical membrane potential assay utilizes voltage-sensitive FRET sensors described by Gonzalez and Tsien (See, Gonzalez, J. E. and R. Y. Tsien (1995) "Voltage sensing by fluorescence resonance energy transfer in single cells” Biophys J 69(4): 1272-80, and Gonzalez, J. E. and R. Y. Tsien (1997) "Improved indicators of cell membrane potential that use fluorescence resonance energy transfer” Chem Biol 4(4): 269-77) in combination with instrumentation for measuring fluorescence changes such as the Voltage/Ion Probe Reader (VIPR) (See, Gonzalez, J. E., K. Oades, et al. (1999) "Cell-based assays and instrumentation for screening ion-channel targets” Drug Discov Today 4(9): 431-439).
  • VIPR Voltage/Ion Probe Reader
  • These voltage sensitive assays are based on the change in fluorescence resonant energy transfer (FRET) between the membrane-soluble, voltage-sensitive dye, DiSBAC 2 (3), and a fluorescent phospholipid, CC2-DMPE, which is attached to the outer leaflet of the plasma membrane and acts as a FRET donor.
  • FRET fluorescence resonant energy transfer
  • V m fluorescent phospholipid
  • the changes in fluorescence emission can be monitored using VEPRTM II, which is an integrated liquid handler and fluorescent detector designed to conduct cell-based screens in 96- or 384-well microtiter plates.
  • the present invention provides a kit for use in measuring the activity of a ABC transporter or a fragment thereof in a biological sample in vitro or in vivo comprising (i) a composition comprising a compound of formula (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B) or any of the above embodiments; and (ii) instructions for a.) contacting the composition with the biological sample and b.) measuring activity of said ABC transporter or a fragment thereof.
  • a kit for use in measuring the activity of a ABC transporter or a fragment thereof in a biological sample in vitro or in vivo comprising (i) a composition comprising a compound of formula (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B) or any of the above embodiments; and (ii) instructions for a.) contacting the composition with the biological sample and b.) measuring activity of said ABC transporter or a fragment thereof.
  • the kit further comprises instructions for a.) contacting an additional composition with the biological sample; b.) measuring the activity qf said ABC transporter or a fragment thereof in the presence of said additional compound, and c.) comparing the activity of the ABC transporter in the presence of the additional compound with the density of the ABC transporter in the presence of a composition of formula (I, II, III, IV, V- A, V-B, I', I'-A, and V-B).
  • the 3dt is used to measure the density of CFTR.
  • Benzyltriethylammonium chloride (0.025 equivalents) and the appropriate dihalo compound (2.5 equivalents) were added to a substituted phenyl acetonitrile.
  • the mixture was heated at 70 0 C and then 50% sodium hydroxide (10 equivalents) was slowly added to the mixture.
  • the reaction was stirred at 70 0 C for 12-24 hours to ensure complete formation of the cycloalkyl moiety and then heated at 130 0 C for 24-48 hours to ensure complete conversion from the nitrile to the carboxylic acid.
  • the dark brown / black reaction mixture was diluted with water and extracted with ethyl acetate and then dichloromethane three times each to remove side products.
  • the basic aqueous solution was acidified with concentrated hydrochloric acid to pH less than one and the precipitate which began to form at pH 4 was filtered and washed with 1 M hydrochloric acid two times.
  • the solid material was dissolved in dichloromethane and extracted two times with 1 M hydrochloric acid and one time with a saturated aqueous solution of sodium chloride.
  • the organic solution was dried over sodium sulfate and evaporated to dryness to give the cycloalkylcarboxylic acid.
  • the dark brown reaction mixture was diluted with water (400 mL) and extracted once with an equal volume of ethyl acetate and once with an equal volume of dichloromethane.
  • the basic aqueous solution was acidified with concentrated hydrochloric acid to pH less than one and the precipitate filtered and washed with 1 M hydrochloric acid.
  • the solid material was dissolved in dichloromethane (400 mL) and extracted twice with equal volumes of 1 M hydrochloric acid and once with a saturated aqueous solution of sodium chloride.
  • Step a 2,2-Difluoro-benzo[l,3]dioxole-5 ⁇ carboxylic acid methyl ester
  • Step b (2,2-Difluoro-benzo[l,3]dioxol-5-yl)-methanol
  • Step d (2,2-Difluoro-benzo[l,3]dioxol-5-yl)-acetonitrile
  • Step e l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarbonitrile
  • Step f l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarboxylic acid l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarbonitrile (crude from the last step) was refluxed in 10% aqueous sodium hydroxide (50 mL) for 2.5 hours. The cooled reaction mixture was washed with ether (100 mL) and the aqueous phase was acidified to pH 2 with 2M hydrochloric acid.
  • Step b 4-Bromomethyl-l-chloro-2-methoxy-benzene
  • Step c 2-(4-Chloro-3-methoxyphenyl)acetonitrile
  • Step a l-(4-Methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester
  • Step b l-(3-Chloromethyl ⁇ 4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester
  • Step c l-(3-Hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester
  • Step d l-[3-( ⁇ ert-Butyl-dimethyl-silanyloxymethyl)-4-methoxy- phenyl]cyclopropane-carboxylic acid methyl ester
  • Step e l-(3-Hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid
  • Step a l-(4-Hydroxy- ⁇ henyl)-cyclopropanecarboxylic acid methyl ester
  • Step b l-(4-Hydroxy-3,5-diiodo-phenyl)-cyclopro ⁇ anecarboxylic acid methyl ester
  • Step c l-[3,5-Diiodo-4-(2-memyl-allyloxy)-phenyl]- cyclopropanecarboxylic acid methyl ester
  • Step d l-(3,3-Dimethyl-2,3-dihydro-benzofuran-5-yl)- cyclopropanecarboxylic acid methyl ester
  • Step e l-(3,3-Dimethyl-2,3-dihydrobenzofuran-5- yl)cyclo ⁇ ropanecarboxylic acid
  • Step b Methyl 7-methoxybenzo[d] [ 1 ,3]dioxole-5-carboxylate
  • Step c (7-Methoxybenzo[d][l,3]dioxol-5-yl)methanol
  • Step d 6-(Chloromethyl)-4-methoxybenzo[d][l,3]dioxole
  • Step e 2-(7-Methoxybenzo[d] [1 ,3]dioxol-5-yl)acetonitrile
  • Step a l-[4-(2,2-Diethoxy-ethoxy)-phenyl]-cyclopropanecarboxylic acid
  • Step b l-Benzofuran-5-yl-cyclopro ⁇ anecarboxylic acid of crude H4-(2,2 ⁇ Ue ⁇ h oxy- e ⁇ hoxy)-ptayI]- cyclopropanecarboxylic acid (20 g, -65 mmol) in xylene (100 mL) was added PPA (22.2 g, 64.9 mmol) at room temperature. The mixture was heated at reflux (140 0 C) for 1 hour before it was cooled to room temperature and decanted from the PPA.
  • Step a (3,4-Dihydroxy- ⁇ henyl)-acetonitrile
  • Step b 2-(2,2-Dimethylbenzo[d][l,3]dioxol-5-yl)acetonitrile
  • Step a (4-Chloro-3-hydroxy-phenyl)acetonitrile
  • Step b 2-(3-(Benzyloxy)-4-chlorophenyl)acetonitrile
  • Step b 2-(Qumolin-6-yl)acetonitrile
  • Step a 2,3-Dihydro ⁇ benzo[l,4]dioxine-6-carboxylic acid ethyl ester
  • Step b (2,3-Dihydro-benzo[l,4]dioxm-6-yl)-methanol
  • Step c 6-Chloromethyl-2,3-dihydro-benzo[l,4]dioxine
  • Step d 2-(2,3-Dihydrobenzo[b][l,4]dioxin-6-yl)acetonitrile
  • a mixture of 6-chloromethyl-2,3-dihydro-benzo[l,4]dioxine (12.5 g, 67.7 mmol) and NaCN (4.30 g, 87.8 mmol) in DMSO (50 mL) was stirred at rt for 1 h. The mixture was poured into water (150 mL) and then extracted with dichloromethane (50 mL x 4).
  • Step a 2,2,4,4-Tetrafluoro-4H-benzo[l,3]dioxine-6-carboxylic acid methyl ester
  • Step b (2,2,4,4-Tetrafluoro-4H-benzo[l,3]dioxin-6-yl)methanol
  • Step c 6-Chloromethyl-2,2,4,4-tetrafluoro-4H-benzo[l,3]dioxine
  • Step d (2,2,4,4-Tetrafluoro-4H-benzo[l,3]dioxin-6-yl)-acetonitrile
  • Step a (3-Hydroxy ⁇ henyl)acetonitrile
  • Step b 2-(4H-Benzo[d] [1 ,3]dioxin-7-yl)acetonitrile
  • paraformaldehyde 84.0 g, 2.80 mol
  • toluene-4-sulfonic acid monohydrate 10.7 g, 56.0 mmol
  • the reaction mixture was heated at reflux for 40 minutes.
  • Toluene was removed by evaporation. Water (150 mL) and ethyl acetate (150 mL) were added.
  • Table 2 Carboxylic acid building blocks.
  • Step a 2,2-Dimethyl-N-(5-methyl-pyridin-2-yl)- ⁇ ro ⁇ iffnide
  • Step b 2,2-Dimethyl-7Y-(5-methyl-l-oxy-pyridin-2-yl)-propionamide
  • Step c N-(6-Chloro-5-methyl-pyridin-2-yl)-2,2-dimethyl-propionamide
  • Ring A is the ring formed by R3 and R'3.
  • X C or N
  • Table 3 Exemplary compounds synthesized according to Preparations W and X.
  • Ring A is the ring formed by R 3 and R' 3 .
  • Step a l-(4-Bromophenylsulfonyl)-4-methylpiperazine
  • Step b l-Methyl-4-[4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2- yl)phenyl]sulfonyl-piperazine
  • the desired product l-methyl-4-[4-(4 ,4,5,5- tetramethyl-l,3,2-dioxaborolan-2-yl)phenyl]-sulfonyl-piperazine
  • the bi-aryl product 4-(4- methylpiperazin-l-ylsulfonyl)-phenyl-phenylsulfonyl-4-methylpiperazine, were obtained in a ratio of 1:2 as indicated by LC/MS analysis. The mixture was used without further purification.
  • Step a 4-Bromophenethyl-4-methylbenzenesulfonate
  • Step b (4-Bromo ⁇ henethyl)(methyl)sulfane
  • Step c l-Bromo-4-(2-methylsulfonyl)-ethylbenzene
  • Step d 4,4,5, 5-Tetramethyl-2-(4-(2-(methylsulfonyl)ethyl)-phenyl)- 1,3,2- dioxaborolane
  • Step a tert-Butyl-4-bromobenzylcarbamate
  • Step b tert-Butyl-4-bromobenzyl(methyl)carbamate
  • fer ⁇ -butyl-4-bromobenzylcarbamate (1.25 g, 4.37 mmol) was dissolved in DMF (12 mL). To this solution was added Ag 2 O (4.0 g, 17 mmol) followed by the addition of CH 3 I (0.68 mL, 11 mmol). The mixture was stirred at 50 0 C for 18 hours. The reaction mixture was filtered through a bed of celite and the celite was washed with methanol (2 x 20 mL) and dichloromethane (2 x 20 mL). The filtrate was concentrated to remove most of the DMF. The residue was treated with water (50 mL) and a white emulsion formed.
  • Step c tert-Butyl 4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2- yl)benzylmethylcarbamate PCTZ OSOGZ Th 11 eO couiSpliBng 11 S r 1 eac + ti.on was ac ,hi.eved , m . , t,he same manner as d ,esc ⁇ .,bed A a u bove f for 1 ⁇ - methyl-4-[4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)phenyl]sulfonyl-piperazine, Preparation AA.
  • the Boc protecting group was removed after the coupling reaction by treating the crude reaction mixture with 0.5 mL of IN HCl in diethyl ether for 18 hours before purification by HPLC.
  • Step a 4-(4,4'-Dimethoxybenzhydryl)-thiophenyl boronic acid
  • Step b 6-(4-(Bis(4-methoxyphenyl)methylthio)phenyl)pyridin-2-amine
  • Step c HBenzo[d][l,3]dioxol-5-yl)-7V-(6-(4-(bis(4- methoxyphenyl)methylthio)phenyl)-pyridin-2-yl)cyclopropanecarboxamide
  • Step d 4-(6-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropane- carboxamido)pyridin-2-yl)benzenesulfonic acid l-(Benzo[d][l,3]dioxol-5-yl)-N-(6-(4-(bis(4-methoxy ⁇ henyl)methylthio)- phenyl)pyridin-2-yl)cyclopropanecarboxamide (-8.5 mmol) was dissolved in AcOH (75 mL) followed by the addition of 30% H 2 O 2 (10 mL). Additional hydrogen peroxide (10 ml) was added 2h later.
  • reaction mixture was stirred at 35-45 °C overnight (-90% conversion, HPLC). The volume of reaction mixture was reduced to a third by evaporation (bath temperature below 40 0 C). The reaction mixture was loaded directly onto a prep RP HPLC column (C-18) and purified. Fractions with 4-(6-(l-(benzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)pyridin-2-yl)benzenesulfonic acid were collected and evaporated r u i ⁇ gfl%f% ⁇ calTbased on 4-mercaptophenylboronic acid). ESI-MS m/z calc. 438.0, found 438.9 (M+l).
  • Step e 4-(6-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopro ⁇ ane- carboxamido)pyridin-2-yl)benzene- 1-sulfonyl chloride
  • Step f l-(Benzo[d][l,3]dioxol-5-yl)-N-(6-(4-(2-methylpyrrolidin-l- ylsulfonyl)phenyl)pyridin-2-yl)cyclopropanecarboxamide
  • Step a (/?)-(l-(4-Bromophenylsulfonyl)pyrrolidin-2-yl)methanol
  • Step b (i?)-(l-(4-bromophenylsulfonyl)pyrrolidin-2-yl)methanol (145 g, crude), which was used in the next step without further purification.
  • 1 H NMR (CDCl 3 , 300 MHz) ⁇ 7.66-7.73 (m, 4 H), 3.59-3.71 (m, 3 H), 3.43-3.51 (m, 1 H), 3.18-3.26 (m, 1 H), 1.680-1.88 (m, 3 H), 1.45-1.53 (m, 1 H).
  • Step b (i?)-l-(4-Bromo-benzenesulfonyl)-2-(te?t-butyl-dimethyl- silanyloxymethyl) pyrrolidine
  • Step c (i?)-4-(2-((fert-butyldimethylsilyloxy)methyl)pyrrolidin-l- ylsulfonyl) phenylboronic acid
  • Step d (6- ⁇ 4-[2-(tert-Butyl-dimethyl-silanyloxymethyl)-pyrrolidine-l- sulfonyl] phenyl ⁇ pyridin-2-yl)carbamic acid tert-butyl ester
  • Step e ⁇ 6-[4-(2-Hydroxymethyl-pyrrolidine-l-sulfonyl)-phenyl]pyridin-
  • Step f (R) -(1-(4-(6-Aminopyridin-2-yl)phenylsulfonyl)-pyrrolidin-2-yl) methanol hydrochloride (C-2)
  • Step a [6-(4-Cyano-phenyl)-pyridin-2-yl]carbamic acid tert-butyl ester
  • Step b [6-(4-Aminomethyl-phenyl)-pyridin-2-yl]-carbamic acid tert- butyl ester
  • Step c ⁇ 6-[4 ⁇ (Methanesulfonylamino-methyl)-phenyl]-pyridin-2- yl ⁇ carbamic acid tert-butyl ester
  • Step d N-(4-(6-Aminopyridin-2-yl)benzyl)methane-sulfonamide (C-3)
  • Step a 4-Bromo-iV-methyl-benzenesulfonamide
  • Step b 4-( ⁇ r -Methylsulfamoyl)phenylboronic acid
  • Step c ⁇ ert-Butyl 6-(4-(iV-methylsulfamoyl)phenyl)pyridin-2-ylcarbamate
  • 4-(7V-methylsulfamoyl)phenylboronic acid (17.2 g, 0.08 mol)
  • (6- bromo-pyridin-2-yl)carbamic acid tert-butyl ester (21.9 g, 0.08 mol)
  • Pd(PPh 3 ) 4 9.2 g, 0.008 mol
  • K 2 CO 3 (16.6 g, 0.12 mol
  • the resulting mixture was degassed by gently bubbling argon through the solution for 5 minutes at 20 0 C.
  • the reaction mixture was then heated at 80 °C for 16 h.
  • the mixture was evaporated under reduced pressure, then poured into H 2 O, and extracted with EtOAc.
  • the organic phase was dried over Na 2 SO 4 , and was evaporated under reduced pressure to give tert-butyl 6-(4-(N- methylsulfamoyl)phenyl)pyridin-2-ylcarbamate (21 g, 58%), which was used in the next step without further purification.
  • Step d 4-(6-Aminopyridin-2-yl)-iV-methylbenzenesulfonamide hydrochloride
  • Additional exemplary compounds 164-388 can also be prepared using appropriate starting materials and methods exemplified for the previously described compounds.
  • Table 7 Physical data for exemplary compounds.
  • the optical membrane potential assay utilized voltage-sensitive FRET sensors described by Gonzalez and Tsien (See, Gonzalez, J. E. and R. Y. Tsien (1995) "Voltage sensing by fluorescence resonance energy transfer in single cells” Biophys J 69(4): 1272-80, and Gonzalez, J. E. and R. Y. Tsien (1997) "Improved indicators of cell membrane potential that use fluorescence resonance energy transfer” Chem Biol 4(4): 269-77) in combination with instrumentation for measuring fluorescence changes such as the Voltage/Ion Probe Reader (VJJPR) (See, Gonzalez, J. E., K. Oades, et al. (1999) "Cell-based assays and instrumentation for screening ion-channel targets” Drug Discov Today 4(9): 431-439).
  • VJJPR Voltage/Ion Probe Reader
  • Chloride-free bath solution Chloride salts in Bath Solution #1 are substituted with gluconate salts.
  • CC2-DMPE Prepared as a 10 mM stock solution in DMSO and stored at -20°C.
  • DiSBAC 2 (3) Prepared as a 10 mM stock in DMSO and stored at
  • NIH3T3 mouse fibroblasts stably expressing ⁇ F508-CFTR are used for optical measurements of membrane potential.
  • the cells are maintained at 37 0 C in 5% CO 2 and 90 % humidity in Dulbecco's modified Eagle's medium supplemented with 2 mM glutamine, 10 % fetal bovine serum, 1 X NEAA, ⁇ -ME, 1 X pen/strep, and 25 mM HEPES in 175 cm 2 culture flasks.
  • the cells were seeded at 30,000/well in 384-well matrigel- coated plates and cultured for 2 hrs at 37 °C before culturing at 27 0 C for 24 hrs for the potentiator assay.
  • the cells are cultured at 27 0 C or 37 °C with and without compounds for 16 - 24 hoursElectrophysiological Assays for assaying ⁇ F508-CFTR modulation properties of compounds
  • the FRT epithelia demonstrated resistances of 4 K ⁇ / cm 2 or more.
  • the solutions were maintained at 27 0 C and bubbled with air.
  • the electrode offset potential and fluid resistance were corrected using a cell-free insert.
  • the current reflects the flow of GT through ⁇ F508-CFTR expressed in the apical membrane.
  • the Isc was digitally acquired using an MPlOOA-CE interface and AcqKnowledge software (v3.2.6; BIOPAC Systems, Santa Barbara, CA).
  • Typical protocol utilized a basolateral to apical membrane Cl " concentration gradient. To set up this gradient, normal ringer was used on the basolateral membrane, whereas apical NaCl was replaced by equimolar sodium gluconate (titrated to pH 7.4 with NaOH) to give a large Cl " concentration gradient across the epithelium. All experiments were performed with intact monolayers. To fully activate ⁇ F5O8-CFTR, forskolin (10 ⁇ M) and the PDE inhibitor, IBMX (100 ⁇ M), were applied followed by the addition of the CFTR potentiator, genistein (50 ⁇ M).
  • Typical protocol utilized a basolateral to apical membrane Cl " concentration gradient.
  • normal ringers was used on the basolateral membrane and was permeabilized with nystatin (360 ⁇ g/ml), whereas apical NaCl was replaced by equimolar sodium gluconate (titrated to pH 7.4 with NaOH) to give a large Cl " concentration gradient across the epithelium. All experiments were performed 30 min after nystatin permeabilization. Forskolin (10 ⁇ M) and all test compounds were added to both sides of the cell culture inserts. The efficacy of the putative ⁇ F508-CFTR potentiators was compared to that of the known potentiator, genistein.
  • Fisher rat epithelial (FRT) cells expressing ⁇ F508-CFTR were used for Ussing chamber experiments for the putative ⁇ F508-CFTR modulators identified from our optical assays.
  • the cells were cultured on Costar Snapwell cell culture inserts and cultured for five days at 37 °C and 5% C ⁇ 2 in Coon's modified Ham's F-12 medium supplemented with 5% fetal calf serum, 100 U/ml penicillin, and 100 ⁇ g/ml streptomycin.
  • the cells Prior to use for characterizing the potentiator activity of compounds, the cells were incubated at 27 0 C for 16 - 48 hrs to correct for the ⁇ F5O8-CFTR. To determine the activity of corrections compounds, the cells were incubated at 27 0 C or 37 °C with and without the compounds for 24 hours.
  • I ⁇ F SOS The macroscopic ⁇ F508-CFTR current (I ⁇ F SOS ) in temperature- and test compound-corrected NIH3T3 cells stably expressing ⁇ F508-CFTR were monitored using the perforated-patch, whole-cell recording.
  • voltage-clamp recordings of I ⁇ F S OS were performed at room temperature using an Axopatch 200B patch-clamp amplifier (Axon Instruments Inc., Foster City, CA). All recordings were acquired at a sampling frequency of 10 kHz and low-pass filtered at 1 kHz. Pipettes had a resistance of 5 - 6 M ⁇ when filled with the intracellular solution.
  • the cells were incubated with 10 ⁇ M of the test compound for 24 hours at 37 0 C and the current density was compared to the 27°C and 37°C controls (% activity). Prior to recording, the cells were washed 3X with extracellular recording medium to remove any remaining test compound. Preincubation with 10 ⁇ M of correction compounds significantly increased the cAMP- and genistein-dependent current compared to the 37°C controls.
  • Intracellular solution in niM: Cs-as ⁇ artate (90), CsCl (50), MgCl 2 (1), HEPES
  • NM3T3 mouse fibroblasts stably expressing ⁇ F508-CFTR are used for whole-cell recordings.
  • the cells are maintained at 37 0 C in 5% CO 2 and 90 % humidity in Dulbecco's modified Eagle's medium supplemented with 2 mM glutamine, 10 % fetal bovine serum, 1 X NEAA, ⁇ -ME, 1 X pen/strep, and 25 mM HEPES in 175 cm 2 culture flasks.
  • 2,500 - 5,000 cells were seeded on poly-L-lysine-coated glass coverslips and cultured for 24 - 48 hrs at 27 °C before use to test the activity of potentiators; and incubated with or without the correction compound at 37 °C.for measuring the activity of correctors.
  • the single-channel actdivities of temperature-corrected ⁇ F508-CFTR stably expressed in NIH3T3 cells and activities of potentiator compounds were observed using excised inside-out membrane patch.
  • voltage-clamp recordings of single-channel activity were performed at room temperature with an Axopatch 200B patch-clamp amplifier (Axon Instruments Inc.). All recordings were acquired at a sampling frequency of 10 kHz and low-pass filtered at 400 Hz.
  • Patch pipettes were fabricated from Corning Kovar Sealing #7052 glass (World Precision Instruments, Inc., Sarasota, FL) and had a resistance of 5 - 8 M ⁇ when filled with the extracellular solution.
  • the ⁇ F508-CFTR was activated after excision, by adding 1 mM Mg-ATP, and 75 nM of the cAMP-dependent protein kinase, catalytic subunit (PKA; Promega Corp. Madison, WI). After channel activity stabilized, the patch was perifused using a gravity-driven microperfusion system. The inflow was placed adjacent to the patch, resulting in complete solution exchange within 1 - 2 sec. To maintain ⁇ F508-CFTR activity during the rapid perifusion, the nonspecific phosphatase inhibitor F " (10 mM NaF) was added to the bath solution. Under these recording conditions, channel activity remained constant throughout the duration of the patch recording (up to 60 min). Currents produced by positive charge moving from the intra- to extracellular solutions (anions moving in the opposite direction) are shown as positive currents. The pipette potential (V p ) was maintained at 80 mV.
  • V p The pipette potential
  • Intracellular solution in mM: NMDG-Cl (150), MgCl 2 (2), EGTA (5), TES (10), and Tris base (14) (pH adjusted to 7.35 with HCl).
  • NIH3T3 mouse fibroblasts stably expressing ⁇ F508-CFTR are used for excised-membrane patch-clamp recordings.
  • the cells are maintained at 37 0 C in 5% CO 2 and 90 % humidity in Dulbecco's modified Eagle's medium supplemented with 2 mM glutamine, 10 % fetal bovine serum, 1 X NEAA, ⁇ -ME, 1 X pen/strep, and 25 mM HEPES in 175 cm 2 culture flasks.
  • 2,500 - 5,000 cells were seeded on poly-L-lysine- coated glass coverslips and cultured for 24 - 48 hrs at 27 °C before use.
  • the exemplified compounds of Table 1 have an activity with a range of about 100 nM and 20 ⁇ M as measured using the assays described hereinabove.
  • the exemplified compounds of Table 1 are found to be sufficiently efficacious as measured using the assays described hereinabove.

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Abstract

Compounds of the present invention, and pharmaceutically acceptable compositions thereof, are useful as modulators of ATP-Binding Cassette ('ABC') transporters or fragments thereof, including Cystic Fibrosis Transmembrane Conductance Regulator ('CFTR'). The present invention also relates to methods of treating ABC transporter mediated diseases using compounds of the present invention.

Description

HETEROCYCLIC MODULATORS OF ATP-BINDING CASSETTE TRANSPORTERS
CROSS-REFERENCE TO RELATED APPLICATIONS
[00100] The present application claims the benefit under 35 U.S. C. § 119 of
United States Provisional Application No. 60/734,506, filed on November 8, 2005, United States Provisional Application No. 60/754,086, filed on December 27, 2005, and United States Provisional Application No. 60/802,458, filed on May 22, 2006, the entire contents of each of the above applications being incorporated herein by reference.
TECHNICAL FIELD OF THE INVENTION
[00101] The present invention relates to modulators of ATP-Binding Cassette
("ABC") transporters or fragments thereof, including Cystic Fibrosis Transmembrane Conductance Regulator ("CFTR"), compositions thereof, and methods therewith. The present invention also relates to methods of treating ABC transporter mediated diseases using such modulators.
BACKGROUND OF THE INVENTION
[00102] ABC transporters are a family of membrane transporter proteins that regulate the transport of a wide variety of pharmacological agents, potentially toxic drugs, and xenobiotics, as well as anions. ABC transporters are homologous membrane proteins that bind and use cellular adenosine triphosphate (ATP) for their specific activities. Some of these transporters were discovered as multi-drug resistance proteins (like the MDRl-P glycoprotein, or the multi-drug resistance protein, MRPl), defending malignant cancer cells against chemotherapeutic agents. To date, 48 ABC Transporters have been identified and grouped into 7 families based on their sequence identity and function.
[00103] ABC transporters regulate a variety of important physiological roles within the body and provide defense against harmful environmental compounds. Because of this, they represent important potential drug targets for the treatment of diseases associated with defects in the transporter, prevention of drug transport out of the target cell, and intervention in other diseases in which modulation of ABC transporter activity may be beneficial.
[00104] One member of the ABC transporter family commonly associated with disease is the cAMP/ATP-mediated anion channel, CFTR. CFTR is expressed in a variety of cells types, including absorptive and secretory epithelia cells, where it regulates anion flux across the membrane, as well as the activity of other ion channels and proteins. In epithelia cells, normal functioning of CFTR is critical for the maintenance of electrolyte transport throughout the body, including respiratory and digestive tissue. CFTR is composed of approximately 1480 amino acids that encode a protein made up of a tandem repeat of transmembrane domains, each containing six transmembrane helices and a nucleotide binding domain. The two transmembrane domains are linked by a large, polar, regulatory (R)-domain with multiple phosphorylation sites that regulate channel activity and cellular trafficking.
[00105] The gene encoding CFTR has been identified and sequenced (See
Gregory, R. J. et al. (1990) Nature 347:382-386; Rich, D. P. et al. (1990) Nature 347:358-362), (Riordan, J. R. et al. (1989) Science 245:1066-1073). A defect in this gene causes mutations in CFTR resulting in Cystic Fibrosis ("CF"), the most common fatal genetic disease in humans. Cystic Fibrosis affects approximately one in every 2,500 infants in the United States. Within the general United States population, up to 10 million people carry a single copy of the defective gene without apparent ill effects. In contrast, individuals with two copies of the CF associated gene suffer from the debilitating and fatal effects of CF, including chronic lung disease.
[00106] In patients with cystic fibrosis, mutations in CFTR endogenously expressed in respiratory epithelia leads to reduced apical anion secretion causing an imbalance in ion and fluid transport. The resulting decrease in anion transport contributes to enhanced mucus accumulation in the lung and the accompanying microbial infections that ultimately cause death in CF patients. In addition to respiratory disease, CF patients typically suffer from gastrointestinal problems and pancreatic insufficiency that, if left untreated, results in death. In addition, the majority of males with cystic fibrosis are infertile and fertility is decreased among females with cystic fibrosis. In contrast to the severe effects of two copies of the CF associated gene, individuals with a single copy of the CF associated gene exhibit increased resistance to cholera and to dehydration resulting from diarrhea - perhaps explaining the relatively high frequency of the CF gene within the population.
[00107] Sequence analysis of the CFTR gene of CF chromosomes has revealed a variety of disease causing mutations (Cutting, G. R. et al. (1990) Nature 346:366-369; Dean, M. et al. (1990) Cell 61:863:870; and Kerem, B-S. et al. (1989) Science 245:1073-1080; Kerem, B- S et al. (1990) Proc. Natl. Acad. Sci. USA 87:8447-8451). To date, > 1000 disease causing mutations in the CF gene have been identified (http://www.genet.sickkids.on.ca/cftr/). The most prevalent mutation is a deletion of phenylalanine at position 508 of the CFTR amino acid sequence, and is commonly referred to as ΔF508-CFTR. This mutation occurs in approximately 70% of the cases of cystic fibrosis and is associated with a severe disease. [00108] The deletion of residue 508 in ΔF508-CFTR prevents the nascent protein from folding correctly. This results in the inability of the mutant protein to exit the ER, and traffic to the plasma membrane. As a result, the number of channels present in the membrane is far less than observed in cells expressing wild-type CFTR. In addition to impaired trafficking, the mutation results in defective channel gating. Together, the reduced number of channels in the membrane and the defective gating lead to reduced anion transport across epithelia leading to defective ion and fluid transport. (Quinton, P. M. (1990), FASEB J. 4: 2709-2727). Studies have shown, however, that the reduced numbers of ΔF508-CFTR in the membrane are functional, albeit less than wild-type CFTR. (Dalemans et al. (1991), Nature Lond. 354: 526- 528; Denning et al., supra; Pasyk and Foskett (1995), J. Cell. Biochem. 270: 12347-50). In addition to ΔF508-CFTR, other disease causing mutations in CFTR that result in defective trafficking, synthesis, and/or channel gating could be up- or down-regulated to alter anion secretion and modify disease progression and/or severity.
[00109] Although CFTR transports a variety of molecules in addition to anions, it is clear that this role (the transport of anions) represents one element in an important mechanism of transporting ions and water across the epithelium. The other elements include the epithelial Na+ channel, ENaC, Na+/2C17K+ co-transporter, Na+-K+-ATPaSe pump and the basolateral membrane K+ channels, that are responsible for the uptake of chloride into the cell.
[00110] These elements work together to achieve directional transport across the epithelium via their selective expression and localization within the cell. Chloride absorption takes place by the coordinated activity of ENaC and CFTR present on the apical membrane and the Na+-K+-ATPase pump and Cl- channels expressed on the basolateral surface of the cell. Secondary active transport of chloride from the luminal side leads to the accumulation of intracellular chloride, which can then passively leave the cell via CF channels, resulting in a vectorial transport. Arrangement of Na+/2C17K+ co-transporter, Na+-K+- ATPase pump and the basolateral membrane K+ channels on the basolateral surface and CFTR on the luminal side coordinate the secretion of chloride via CFTR on the luminal side. Because water is probably never actively transported itself, its flow across epithelia depends on tiny transepithelial osmotic gradients generated by the bulk flow of sodium and chloride.
[00111] In addition to Cystic Fibrosis, modulation of CFTR activity may be beneficial for other diseases not directly caused by mutations in CFTR, such as secretory diseases and other protein folding diseases mediated by CFTR. These include, but are not limited to, chronic obstructive pulmonary disease (COPD), dry eye disease, and Sjogren's Syndrome. [00112] COPD is characterized by airflow limitation that is progressive and not fully reversible. The airflow limitation is due to mucus hypersecretion, emphysema, and bronchiolitis. Activators of mutant or wild-type CFTR offer a potential treatment of mucus hypersecretion and impaired mucociliary clearance that is common in COPD. Specifically, increasing anion secretion across CFTR may facilitate fluid transport into the airway surface liquid to hydrate the mucus and optimized periciliary fluid viscosity. This would lead to enhanced mucociliary clearance and a reduction in the symptoms associated with COPD. Dry eye disease is characterized by a decrease in tear aqueous production and abnormal tear film lipid, protein and mucin profiles. There are many causes of dry eye, some of which include age, Lasik eye surgery, arthritis, medications, chemical/thermal burns, allergies, and diseases, such as Cystic Fibrosis and Sjδgrens's syndrome. Increasing anion secretion via CFTR would enhance fluid transport from the corneal endothelial cells and secretory glands surrounding the eye to increase corneal hydration. This would help to alleviate the symptoms associated with dry eye disease. Sjδgrens's syndrome is an autoimmune disease in which the immune system attacks moisture-producing glands throughout the body, including the eye, mouth, skin, respiratory tissue, liver, vagina, and gut. Symptoms, include, dry eye, mouth, and vagina, as well as lung disease. The disease is also associated with rheumatoid arthritis, systemic lupus, systemic sclerosis, and polymypositis/dermatomyositis. Defective protein trafficking is believed to cause the disease, for which treatment options are limited. Modulators of CFTR activity may hydrate the various organs afflicted by the disease and help to elevate the associated symptoms.
[00113] As discussed above, it is believed that the deletion of residue 508 in
ΔF508-CFTR prevents the nascent protein from folding correctly, resulting in the inability of this mutant protein to exit the ER, and traffic to the plasma membrane. As a result, insufficient amounts of the mature protein are present at the plasma membrane and chloride transport within epithelial tissues is significantly reduced. In fact, this cellular phenomenon of defective ER processing of ABC transporters by the ER machinery has been shown to be the underlying basis not only for CF disease, but for a wide range of other isolated and inherited diseases. The two ways that the ER machinery can malfunction is either by loss of coupling to ER export of the proteins leading to degradation, or by the ER accumulation of these defective/misfolded proteins [Aridor M, et al, Nature Med., 5(7), pp 745- 751 (1999); Shastry, B.S., et al, Neurochem. International, 43, pp 1-7 (2003); Rutishauser, J., et al., Swiss Med WkIy, 132, pp 211-222 (2002); Morello, JP et al, TIPS, 21, pp. 466- 469 (2000); Bross P., et al, Human Mut., 14, pp. 186-198 (1999)]. The diseases associated with the first class of ER malfunction are Cystic fibrosis (due to misfolded ΔF508-CFTR as discussed above), Hereditary emphysema (due to al-antitrypsin; non Piz variants), Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses (due to Lysosomal processing enzymes), Sandhof/Tay-Sachs (due to β- Hexosaminidase), Crigler-Najjar type II (due to UDP-glucuronyl-sialyc-transferase), Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus (due to Insulin receptor), Laron dwarfism (due to Growth hormone receptor), Myleoperoxidase deficiency, Primary hypoparathyroidism (due to Preproparathyroid hormone), Melanoma (due to Tyrosinase). The diseases associated with the latter class of ER malfunction are Glycanosis CDG type 1, Hereditary emphysema (due to αl -Antitrypsin (PiZ variant), Congenital hyperthyroidism, Osteogenesis imperfecta (due to Type I, II, IV procollagen), Hereditary hypofibrinogenemia (due to Fibrinogen), ACT deficiency (due to αl-Antichymotrypsin), Diabetes insipidus (DI), Neurophyseal DI (due to Vasopvessin hormone/ V2-receptor), Neprogenic DI (due to Aquaporin II), Charcot-Marie Tooth syndrome (due to Peripheral myelin protein 22), Perlizaeus- Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease ( due to βAPP and presenilins), Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, Spinocerebullar ataxia type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt- Jakob disease (due to Prion protein processing defect), Fabry disease (due to lysosomal α-galactosidase A) and Straussler-Scheinker syndrome (due to Prp processing defect).
[00114] In addition to up-regulation of CFTR activity, reducing anion secretion by CFTR modulators may be beneficial for the treatment of secretory diarrheas, in which epithelial water transport is dramatically increased as a result of secretagogue activated chloride transport. The mechanism involves elevation of cAMP and stimulation of CFTR.
[00115] Although there are numerous causes of diarrhea, the major consequences of diarrheal diseases, resulting from excessive chloride transport are common to all, and include dehydration, acidosis, impaired growth and death.
[00116] Acute and chronic diarrheas represent a major medical problem in many areas of the world. Diarrhea is both a significant factor in malnutrition and the leading cause of death (5,000,000 deaths/year) in children less than five years old. [00117] ■ Secretory diarrheas are also a dangerous condition in patients of acquired immunodeficiency syndrome (ADDS) and chronic inflammatory bowel disease (EBD). 16 million travelers to developing countries from industrialized nations every year develop diarrhea, with the severity and number of cases of diarrhea varying depending on the country and area of travel.
[00118] Diarrhea in barn animals and pets such as cows, pigs, and horses, sheep, goats, cats and dogs, also known as scours, is a major cause of death in these animals. Diarrhea can result from any major transition, such as weaning or physical movement, as well as in response to a variety of bacterial or viral infections and generally occurs within the first few hours of the animal's life.
[00119] The most common diarrhea causing bacteria is enterotoxogenic E-coli
(ETEC) having the K99 pilus antigen. Common viral causes of diarrhea include rotavirus and coronavirus. Other infectious agents include Cryptosporidium, giardia lamblia, and salmonella, among others.
[00120] Symptoms of rotaviral infection include excretion of watery feces, dehydration and weakness. Coronavirus causes a more severe illness in the newborn animals, and has a higher mortality rate than rotaviral infection. Often, however, a young animal may be infected with more than one virus or with a combination of viral and bacterial microorganisms at one time. This dramatically increases the severity of the disease.
[00121] Accordingly, there is a need for modulators of an ABC transporter activity, and compositions thereof, that can be used to modulate the activity of the ABC transporter in the cell membrane of a mammal.
[00122] There is a need for methods of treating ABC transporter mediated diseases using such modulators of ABC transporter activity.
[00123] There is a need for methods of modulating an ABC transporter activity in an ex vivo cell membrane of a mammal.
[00124] There is a need for modulators of CFTR activity that can be used to modulate the activity of CFTR in the cell membrane of a mammal.
[00125] There is a need for methods of treating CFTR-mediated diseases using such modulators of CFTR activity.
[00126] There is a need for methods of modulating CFTR activity in an ex vivo cell membrane of a mammal. SUMMARY OP THE INVENTION
[00127] It has now been found that compounds of this invention, and pharmaceutically acceptable compositions thereof, are useful as modulators of ABC transporter activity. These compounds have the general formula (I):
Figure imgf000008_0001
(D or a pharmaceutically acceptable salt thereof, wherein Ri, R2, R3, R!3, R4, and n are described herein.
[00128] These compounds and pharmaceutically acceptable compositions are useful for treating or lessening the severity of a variety of diseases, disorders, or conditions, including, but not limited to, cystic fibrosis, hereditary emphysema, hereditary hemochromatosis, coagulation-fibrinolysis deficiencies, such as protein C deficiency, Type 1 hereditary angioedema, lipid processing deficiencies, such as familial hypercholesterolemia, Type 1 chylomicronemia, abetalipoproteinemia, lysosomal storage diseases, such as I-cell disease/pseudo-Hurler, mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, polyendocrinopathy/hyperinsulemia, Diabetes Mellitus, Laron dwarfism, myleoperoxidase deficiency, primary hypoparathyroidism, melanoma, glycanosis CDG type 1, hereditary emphysema, congenital hyperthyroidism, osteogenesis imperfecta, hereditary hypofibrinogenemia, ACT deficiency, Diabetes Insipidus (DI), neurophyseal DI, neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, spinocerebullar ataxia type I, spinal and bulbar muscular atrophy, dentatorubal pallidoluysian, and myotonic dystrophy, as well as spongiform encephalopathies, such as hereditary Creutzfeldt- Jakob disease, Fabry disease, Straussler-Scheinker syndrome, COPD, dry-eye disease, and Sjogren's disease.
DETAILED DESCRIPTION OF THE INVENTION DEFINITIONS
[00129] As used herein, the following definitions shall apply unless otherwise indicated. [00130] The term "ABC-transporter" as used herein means an ABC-transporter protein or a fragment thereof comprising at least one binding domain, wherein said protein or fragment thereof is present in vivo or in vitro. The term "binding domain" as used herein means a domain on the ABC-transporter that can bind to a modulator. See, e.g., Hwang, T. C. et al., J. Gen. Physiol. (1998): 111(3), 477-90.
[00131] The term "CFTR" as used herein means cystic fibrosis transmembrane conductance regulator or a mutation thereof capable of regulator activity, including, but not limited to, ΔF508 CFTR and G551D CFTR (see, e.g., http://www.genet.sickkids.on.ca/cftr/, for CFTR mutations).
[00132] The term "modulating" as used herein means increasing or decreasing, e.g. activity, by a measurable amount. Compounds that modulate ABC Transporter activity, such as CFTR activity, by increasing the activity of the ABC Transporter, e.g., a CFTR anion channel, are called agonists. Compounds that modulate ABC Transporter activity, such as CFTR activity, by decreasing the activity of the ABC Transporter, e.g., CFTR anion channel, are called antagonists. An agonist interacts with an ABC Transporter, such as CFTR anion channel, to increase the ability of the receptor to transduce an intracellular signal in response to endogenous ligand binding. An antagonist interacts with an ABC Transporter, such as CFTR, and competes with the endogenous ligand(s) or substrate(s) for binding site(s) on the receptor to decrease the ability of the receptor to transduce an intracellular signal in response to endogenous ligand binding.
[00133] The phrase "treating or reducing the severity of an ABC Transporter mediated disease" refers both to treatments for diseases that are directly caused by ABC Transporter and/or CFTR activities and alleviation of symptoms of diseases not directly caused by ABC Transporter and/or CFTR anion channel activities. Examples of diseases whose symptoms may be affected by ABC Transporter and/or CFTR activity include, but are not limited to, Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation- Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1, Hereditary emphysema, Congenital hyperthyroidism, Osteogenesis imperfecta, Hereditary hypofibrinogenemia, ACT deficiency, Diabetes insipidus (DI), Neurophyseal DI, Neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, Spinocerebullar ataxia type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt- Jakob disease, Fabry disease, Straussler-Scheinker syndrome, COPD, dry-eye disease, and Sjogren's disease.
[00134] For purposes of this invention, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed. Additionally, general principles of organic chemistry are described in "Organic Chemistry", Thomas Sorrell, University Science Books, Sausolito: 1999, and "March's Advanced Organic Chemistry", 5th Ed., Ed.: Smith, M.B. and March, J., John Wiley & Sons, New York: 2001, the entire contents of which are hereby incorporated by reference.
[00135] For purposes of this invention, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed. Additionally, general principles of organic chemistry are described in "Organic Chemistry", Thomas Sorrell, University Science Books, Sausalito: 1999, and "March's Advanced Organic Chemistry", 5th Ed., Ed.: Smith, M.B. and March, J., John Wiley & Sons, New York: 2001.
[00136] As used herein the term "aliphatic' encompasses the terms alkyl, alkenyl, alkynyl, each of which being optionally substituted as set forth below.
[00137] As used herein, an "alkyl" group refers to a saturated aliphatic hydrocarbon group containing 1-8 (e.g., 1-6 or 1-4) carbon atoms. An alkyl group can be straight or branched. Examples of alkyl groups include, but are not limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, n-heptyl, or 2-ethylhexyl. An alkyl group can be substituted (i.e., optionally substituted) with one or more substituents such as halo, cycloaliphatic [e.g., cycloalkyl or cycloalkenyl], heterocycloaliphatic [e.g., heterocycloalkyl or heterocycloalkenyl], aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, acyl [e.g., (aliphatic)c.arbonyl, (cycloaliphatic)carbonyl, or (heterocycloaliphatic)carbonyl], nitro, cyano, amido [e.g., (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, heteroaralkylcarbonylamino], amino [e.g., aliphaticamino, cycloaliphaticamino, or heterocycloaliphaticamino], sulfonyl [e.g., aliphaticsulfonyl], sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, cycloaliphaticoxy, heterocycloaliphaticoxy, aryloxy, heteroaryloxy, aralkyloxy, heteroarylalkoxy, alkoxycarbonyl, alkylcarbonyloxy, or hydroxy. Without limitation, some examples of substituted alkyls include carboxyalkyl (such as HOOC-alkyl, alkoxycarbonylalkyl, and alkylcarbonyloxyalkyl), cyanoalkyl, hydroxyalkyl, alkoxyalkyl, acylalkyl, hydroxyalkyl, aralkyl, (alkoxyaryl)alkyl, (sulfonylamino)alkyl (such as (alkylsulfonylamino)alkyl), aminoalkyl, amidoalkyl, (cycloaliphatic)alkyl, cyanoalkyl, or haloalkyl.
[00138] As used herein, an "alkenyl" group refers to an aliphatic carbon group that contains 2-8 (e.g., 2-6 or 2-4) carbon atoms and at least one double bond. Like an alkyl group, an alkenyl group can be straight or branched. Examples of an alkenyl group include, but are not limited to, allyl, isoprenyl, 2-butenyl, and 2-hexenyl. An alkenyl group can be optionally substituted with one or more substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, acyl [e.g., (cycloaliphatic)carbonyl, or (heterocycloaliphatic)carbonyl], nitro, cyano, acyl [e.g., aliphaticcarbonyl, cycloaliphaticcarbonyl, arylcarbonyl, heterocycloaliphaticcarbonyl or heteroarylcarbonyl], amido [e.g., (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino,
(heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, heteroaralkylcarbonylamino alkylaminocarbonyl, cycloalkylaminocarbonyl, heterocycloalkylaminocarbonyl, arylaminocarbonyl, or heteroarylaminocarbonyl], amino [e.g., aliphaticamino, or aliphaticsulfonylamino], sulfonyl [e.g., alkylsulfonyl, cycloaliphaticsulfonyl, or arylsulfonyl], sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, cycloaliphaticoxy, heterocycloaliphaticoxy, aryloxy, heteroaryloxy, aralkyloxy, heteroarylalkoxy, alkoxycarbonyl, alkylcarbonyloxy, or hydroxy.
[00139] As used herein, an "alkynyl" group refers to an aliphatic carbon group that contains 2-8 (e.g., 2-6 or 2-4) carbon atoms and has at least one triple bond. An alkynyl group can be straight or branched. Examples of an alkynyl group include, but are not limited to, propargyl and butynyl. An alkynyl group can be optionally substituted with one or more substituents such as aroyl, heteroaroyl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, nitro, carboxy, cyano, halo, hydroxy, sulfo, mercapto, sulfanyl [e.g., aliphaticsulfanyl or cycloaliphaticsulfanyl], sulfinyl [e.g., aliphaticsulfinyl or cycloaliphaticsulfinyl], sulfonyl [e.g., aliphaticsulfonyl, aliphaticaminosulfonyl, or cycloaliphaticsulfonyl], amido [e.g., aminocarbonyl, alkylaminocarbonyl, alkylcarbonylamino, cycloalkylaminocarbonyl, heterocycloalkylaminocarbonyl, cycloalkylcarbonylamino, arylaminocarbonyl, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkytycarbonylamino, (cycloalkylalky^carbonylamino, heteroaralkylcarbonylamino, heteroarylcarbonylamino or heteroarylaminocarbonyl], urea, thiourea, sulfamoyl, sulfamide, alkoxycarbonyl, alkylcarbonyloxy, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, acyl [e.g., (cycloaliphatic)carbonyl or (heterocycloaliphatic)carbonyl], amino [e.g., aliphaticamino], sulfoxy, oxo, carboxy, carbamoyl, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, or (heteroaryl)alkoxy.
[00140] As used herein, an "amido" encompasses both "aminocarbonyl" and
"carbonylamino". These terms when used alone or in connection with another group refers to an amido group such as N(RXRY)-C(O)- or RYC(O)-N(RX)- when used terminally and -C(O)- N(RX)- or -N(RX)-C(O)- when used internally, wherein Rx and Rγ are defined below. Examples of amido groups include alkylamido (such as alkylcarbonylamino or alkylcarbonylamino), (heterocycloaliphatic)amido, (heteroaralkyl)amido, (heteroaryl)amido, (heterocycloalkyl)alkylamido, arylamido, aralkylamido, (cycloalkyl)alkylamido, or cycloalkylamido.
[00141] As used herein, an "amino" group refers to -NR R wherein each of R and Rγ is independently hydrogen, alkyl, cycloaliphatic, (cycloaliphatic)aliphatic, aryl, araliphatic, heterocycloaliphatic, (heterocycloaliphatic)aliphatic, heteroaryl, carboxy, sulfanyl, sulfinyl, sulfonyl, (aliphatic)carbonyl, (cycloaliphatic)carbonyl, ((cycloaliphatic)aliphatic)carbonyl, arylcarbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, (heteroaryl)carbonyl, or (heteroaraliphatic)carbonyl, each of which being defined herein and being optionally substituted. Examples of amino groups include alkylamino, dialkylamino, or arylamino. When the term "amino" is not the terminal group (e.g., alkylcarbonylamino), it is represented by - NRX-. Rx has the same meaning as defined above.
[00142] As used herein, an "aryl" group used alone or as part of a larger moiety as in "aralkyl", "aralkoxy", or "aryloxyalkyl" refers to monocyclic (e.g., phenyl); bicyclic (e.g., indenyl, naphthalenyl, tetrahydronaphthyl, tetrahydroindenyl); and tricyclic (e.g., fluorenyl tetrahydrofluorenyl, or tetrahydroanthracenyl, anthracenyl) ring systems in which the monocyclic ring system is aromatic or at least one of the rings in a bicyclic or tricyclic ring system is aromatic. The bicyclic and tricyclic ring systems include benzofused 2-3 membered carbocyclic rings. For example, a benzofused group includes phenyl fused with two or more C4- 8 carbocyclic moieties. An aryl is optionally substituted with one or more substituents including aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliphatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic ring of a benzofused bicyclic or tricyclic aryl); nitro; carboxy; amido; acyl [ e.g., aliphaticcarbonyl; (cycloaliphatic)carbonyl; ((cycloaliphatic)aliphatic)carbonyl; (araliphatic)carbonyl; (heterocycloaliphatic)carbonyl; ((heterocycloaliphatic)aliphatic)carbonyl; or (heteroaraliρhatic)carbonyl]; sulfonyl [e.g., aliphaticsulfonyl or aminosulfonyl]; sulfinyl [e.g., aliphaticsulfmyl or cycloaliphaticsulfmyl]; sulfanyl [e.g., aliphaticsulfaπyl]; cyano; halo; hydroxy; mercapto; sulfoxy; urea; thiourea; sulfamoyl; sulfamide; or carbamoyl. Alternatively, an aryl can be unsubstituted.
[00143] Non-limiting examples of substituted aryls include haloaryl [e.g., mono-, di ( such as/VTz-dihaloaryl), and (trihalo)aryl]; (carboxy)aryl [e.g., (alkoxycarbonyl)aryl, ((aralkyi)carbonyloxy)aryl, and (alkoxycarbonyl)aryl]; (amido)aryl [e.g., (aminocarbonyl)aryl, (((alkylamino)aϊkyl)aminocarbonyl)aryl, (alkylcarbonyl)aminoaryl, (arylaminocarbonyl)aryl, and (((heteroaryl)amino)carbonyl)aryl]; aminoaryl [e.g., ((alkylsulfonyl)amino)aryl or ((dialkyl)amino)aryl]; (cyanoalkyl)aryl; (alkoxy)aryl; (sulfamoyl)aryl [e.g., (aminosulfonyl)aryl]; (alkylsulfonyl)aryl; (cyano)aryl; (hydroxyalkyl)aryl; ((alkoxy)alkyl)aryl; (hydroxy)aryl, ((carboxy)alkyl)aryl; (((dialkyl)amino)alkyl)aryl; (nitroalkyl)aryl; (((alkylsulfonyl)amino)alkyl)aryl; ((heterocycloaliphatic)carbonyl)aryl; ((alkylsulfonyl)alkyl)aryl; (cyanoalkyl)aryl; (hydroxyalkyl)aryl; (alkylcarbonyl)aryl; alkylaryl; (trihaloalkyl)aryl; p-amino-m-alkoxycarbonylaryl; p-amino-m-cyanoaryl; p-halo-m-aminoaryl; or (in-(heterocycloaliphatic)-o-(alkyl))aryl .
[00144] As used herein, an "araliphatic" such as an "aralkyl" group refers to an aliphatic group (e.g., a Ci-4 alkyl group) that is substituted with an aryl group. "Aliphatic," "alkyl," and "aryl" are defined herein. An example of an araliphatic such as an aralkyl group is benzyl.
[00145] As used herein, an "aralkyl" group refers to an alkyl group (e.g., a Ci-4 alkyl group) that is substituted with an aryl group. Both "alkyl" and "aryl" have been defined above. An example of an aralkyl group is benzyl. An aralkyl is optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl, including carboxyalkyl, hydroxyalkyl, or haloalkyl such as trifluoromethyl], cycloaliphatic [e.g., cycloalkyl or cycloalkenyl], (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, amido [e.g., aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylarnino, (cycloalkylalky^carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkytycarbonylamino, (heterocycloalkylalkytycarbonylamino, heteroarylcarbonylamino, or heteroaralkylcarbonylamino], cyano, halo, hydroxy, acyl, mercapto, alkylsulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl.
[00146] As used herein, a "bicyclic ring system" includes 8-12 (e.g., 9, 10, or 11) membered structures that form two rings, wherein the two rings have at least one atom in common (e.g., 2 atoms in common). Bicyclic ring systems include bicycloaliphatics (e.g., bicycloalkyl or bicycloalkenyl), bicycloheteroaliphatics, bicyclic aryls, and bicyclic heteroaryls.
[00147] As used herein, a "cycloaliphatic" group encompasses a "cycloalkyl" group and a "cycloalkenyl" group, each of which being optionally substituted as set forth below.
[00148] As used herein, a "cycloalkyl" group refers to a saturated carbocyclic mono- or bicyclic (fused or bridged) ring of 3-10 (e.g., 5-10) carbon atoms. Examples of cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, norbornyl, cubyl, octahydro-indenyl, decahydro-naphthyl, bicyclo[3.2.1]octyl, bicyclo[2.2.2]octyl, bicyclo[3.3.1]nonyl, bicyclo[3.3.2.]decyl, bicyclo[2.2.2]octyl, adamantyl, azacycloalkyl, or ((aminocarbonyl)cycloalkyl)cycloalkyl. A "cycloalkenyl" group, as used herein, refers to a non-aromatic carbocyclic ring of 3-10 (e.g., 4-8) carbon atoms having one or more double bonds. Examples of cycloalkenyl groups include cyclopentenyl, 1,4-cyclohexa-di- enyl, cycloheptenyl, cyclooctenyl, hexahydro-indenyl, octahydro-naphthyl, cyclohexenyl, cyclopentenyl, bicyclo[2.2.2]octenyl, or bicyclo[3.3.1]nonenyl. A cycloalkyl or cycloalkenyl group can be optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic) aliphatic, heterocycloaliphatic, (heterocycloaliphatic) aliphatic, aryl, heteroaryl, alkoxy, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliphatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic )carbonylamino,
(cycloaliphatic)carbonylamino, ((cycloaliphatic)aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (heterocycloaliphatic)carbonylamino, ((heterocycloaliphatic)aliphatic)carbonylamino, (heteroaryl)carbonylamino, or (heteroaraliphatic)carbonylamino], nitro, carboxy [e.g., HOOC-, alkoxycarbonyl, or alkylcarbonyloxy], acyl [e.g., (cycloaliρhatic)carbonyl, ((cycloaliphatic) aliphatic)carbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, or (heteroaraliphatic)carbonyl], cyano, halo, hydroxy, mercapto, sulfonyl [e.g., alkylsulfonyl and arylsulfonyl], sulfinyl [e.g., alkylsulfinyl], sulfanyl [e.g., alkylsulfanyl], sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl.
[00149] As used herein, "cyclic moiety" includes cycloaliphatic, heterocycloaliphatic, aryl, or heteroaryl, each of which has been defined previously.
[00150] As used herein, the term "heterocycloaliphatic" encompasses a heterocycloalkyl group and a heterocycloalkenyl group, each of which being optionally substituted as set forth below.
[00151] As used herein, a "heterocycloalkyl" group refers to a 3-10 membered mono- or bicylic (fused or bridged) (e.g., 5- to 10-membered mono- or bicyclic) saturated ring structure, in which one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof). Examples of a heterocycloalkyl group include piperidyl, piperazyl, tetrahydropyranyl, tetrahydrofuryl, 1,4-dioxolanyl, 1,4-dithianyl, 1,3-dioxoIanyl, oxazolidyl, isoxazolidyl, morpholinyl, thiomorpholyl, octatvydrobenzofuryl, octahydrochromenyl, octahydrothiochromenyl, octahydroindolyl, octahydropyrindinyl, decahydroquinolinyl, octahydrobenzo[&]thiopheneyl, 2-oxa-bicyclo[2.2.2]octyl, l-aza-bicyclo[2.2.2]octyl, 3-aza- bicyclo[3.2.1]octyl, and 2,6-dioxa-tricyclo[3.3.1.03'7]nonyl. A monocyclic heterocycloalkyl group can be fused with a phenyl moiety such as tetrahydroisoquinoline. A "heterocycloalkenyl" group, as used herein, refers to a mono- or bicylic (e.g., 5- to 10- membered mono- or bicyclic) non-aromatic ring structure having one or more double bonds, and wherein one or more of the ring atoms is a heteroatom (e.g., N, O, or S). Monocyclic and bicycloheteroaliphatics are numbered according to standard chemical nomenclature.
[00152] A heterocycloalkyl or heterocycloalkenyl group can be optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic)aliρhatic, heterocycloaliphatic, (heterocycloaliphatic)aliphatic, aryl, heteroaryl, alkoxy, (cycloaliρhatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliρhatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic)carbonylamino, (cycloaliphatic)carbonylarnino, ((cycloaliphatic) aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (heterocycloaliphatic)carbonylamino, ((heterocycloaliphatic) aliphatic)carbonylamino, (heteroaryl)carbonylarnino, or (heteroaraliρhatic)carbonylamino], nitro, carboxy [e.g., HOOC-, alkoxycarbonyl, or alkylcarbonyloxy], acyl [e.g., (cycloaliphatic)carbonyl, ((cycloaliphatic) aliphatic)carbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, or (heteroaraliphatic)carbonyl], nitro, cyano, halo, hydroxy, mercapto, sulfonyl [e.g., alkylsulfonyl or arylsulfonyl], sulfinyl [e.g., alkylsulfinyl], sulfanyl [e.g., alkylsulfanylj, sulfoxy, urea, thiourea, sulfamoyl, sulfarnide, oxo, or carbamoyl.
[00153] A "heteroaryl" group, as used herein, refers to a monocyclic, bicyclic, or tricyclic ring system having 4 to 15 ring atoms wherein one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof) and in which the monocyclic ring system is aromatic or at least one of the rings in the bicyclic or tricyclic ring systems is aromatic. A heteroaryl group includes a benzofused ring system having 2 to 3 rings. For example, a benzofused group includes benzo fused with one or two 4 to S rnembered heterocycloaliphatic moieties (e.g., indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo[ib]furyl, benzo[&]thiophenyl, quinolinyl, or isoquinolinyl). Some examples of heteroaryl are azetidinyl, pyridyl, lH-indazolyl, furyl, pyrrolyl, thienyl, thiazolyl, oxazolyl, irαidazolyl, tetrazolyl, benzofuryl, isoquinolinyl, benzthiazolyl, xanthene, thioxanthene, phenothiazine, dihydroindole, benzo[l,3]dioxole, benzo[b]furyl, benzo[b]thiophenyl, indazolyl, benzimidazolyl, benzthiazolyl, puryl, cinnolyl, quinolyl, quinazolyl,cinnolyl, phthalazyl, quinazolyl, quinoxalyl, isoquinolyl, 4H-quinolizyl, benzo-l,2,5-thiadiazolyl, or 1,8-naphthyridyl.
[00154] Without limitation, monocyclic heteroaryls include furyl, thiophenyl, 2H- pyrrolyl, pyrrolyl, oxazolyl, thazolyl, imidazolyl, pyrazolyl, isoxazolyl, isothiazolyl, 1,3,4- thiadiazolyl, 2H-pyranyl, 4-H-pyranyl, pyridyl, pyridazyl, pyrimidyl, pyrazolyl, pyrazyl, or 1,3,5-triazyl. Monocyclic heteroaryls are numbered according to standard chemical nomenclature.
[00155] Without limitation, bicyclic heteroaryls include indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo [6]furyl, benzo[έ]thiophenyl, quinolinyl, isoquinolinyl, indolizyl, isoindolyl, indolyl, benzo[&]furyl, beχo[£]thioρhenyl, indazolyl, benzimidazyl, benzthiazolyl, purinyl, 4H-quinolizyl, quinolyl, isoquinolyl, cinnolyl, phthalazyl, quinazolyl, quinoxalyl, 1,8-naphthyridyl, or pteridyl. Bicyclic heteroaryls are numbered according to standard chemical nomenclature.
[00156] A heteroaryl is optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliρhatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic or heterocyclic ring of a bicyclic or tricyclic heteroaryl); carboxy; amido; acyl [ e.g., aliphaticcarbonyl; (cycloaliphatic)carbonyl; ((cycloaliphatic)aliρhatic)carbonyl; (araliphatic)carbortyl; (heterocycloaliphatic)carbonyl; ((heterocycloaliphatic)aliphatic)carbonyl; or (heteroaraliphatic)carbonyl]; sulfonyl [e.g., aliphaticsulfonyl or aniinosulfonylj; sulfinyl [e.g., aliphaticsulfinyl]; sulfanyl [e.g., aliphaticsulfanyl]; nitro; cyano; halo; hydroxy; mercapto; sulfoxy; urea; thiourea; sulfamoyl; sulfamide; or carbamoyl. Alternatively, a heteroaryl can be unsubstituted.
[00157] Non-limiting examples of substituted heteroaryls include (halo)heteroaryl
[e.g., mono- and di~(halo)heteroaryl]; (carboxy)heteroaryl [e.g., (alkoxycarbonyl)heteroaryl]; cyanoheteroaryl; aminoheteroaryl [e.g., ((alkylsulfonyl)amino)heteroaryl and((dialkyl)amino)heteroaryl]; (amido)heteroaryl [e.g., aminocarbonylheteroaryl, ((alkylcarbonyl)amino)heteroaryl, ((((alkyl)amino)alkyl)aminocarbonyl)heteroaryl, (((heteroaryl)amino)carbonyl)heteroaryl, ((heterocycloaliphatic)carbonyl)heteroaryl, and ((alkylcarbonyl)amino)heteroaryl] ; (cyanoalkyl)heteroaryl; (alkoxy)heteroaryl; (sulfamoyl)heteroaryl [e.g., (aminosulfonyl)heteroaryl]; (sulfonyl)heteroaryl [e.g., (alkylsulf onyl)heteroaryl] ; (hydroxyalkyl)heteroaryl ; (alkoxyalkyl)heteroaryl; (hydroxy)heteroaryl; ((carboxy)alkyl)heteroaryl; [((dialkyl)amino)alkyl]heteroaryl; (heterocycloaliphatic)heteroaryl; (cycloaliphatic)heteroaryl; (nitroalkyl)heteroaryl; (((alkylsulfonyl)amino)alkyl)heteroaryl; ((alkylsulfonyl)alkyl)heteroaryl; (cyanoalkyl)heteroaryl; (acyl)heteroaryl [e.g., (alkylcarbonyl)heteroaryl]; (alkyl)heteroaryl, and (haloalkyl)heteroaryl [e.g., trihaloalkylheteroaryl].
[00158] A "heteroaraliphatic" (such as a heteroaralkyl group) as used herein, refers to an aliphatic group (e.g., a C1-4 alkyl group) that is substituted with a heteroaryl group. "Aliphatic," "alkyl," and "heteroaryl" have been defined above.
[00159] A "heteroaralkyl" group, as used herein, refers to an alkyl group (e.g., a
C1-4 alkyl group) that is substituted with a heteroaryl group. Both "alkyl" and "heteroaryl" have been defined above. A heteroaralkyl is optionally substituted with one or more substituents such as alkyl (including carboxyalkyl, hydroxyalkyl, and haloalkyl such as trifluoromethyl), alkenyl, alkynyl, cycloalkyl, (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylamino, (cycloalkylalky^carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyOcarbonylamino, (heterocycloalkylalky^carbonylamino, heteroarylcarbonylamino, heteroaralkylcarbonylamino, cyano, halo, hydroxy, acyl, mercapto, alkylsulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl. [00160] As used herein, "cyclic moiety" includes cycloalkyl, heterocycloalkyl, cycloalkenyl, heterocycloalkenyl, aryl, or heteroaryl, each of which has been defined previously.
[00161] As used herein, an "acyl" group refers to a formyl group or RX-C(O)-
(such as -alkyl-C(O)-, also referred to as "alkylcarbonyl") where Rx and "alkyl" have been defined previously. Acetyl and pivaloyl are examples of acyl groups.
[00162] As used herein, an "aroyl" or "heteroaroyl" refers to an aryl-C(O)- or a heteroaryl-C(O)-. The aryl and heteroaryl portion of the aroyl or heteroaroyl is optionally substituted as previously defined.
[00163] As used herein, an "alkoxy" group refers to an alkyl-O- group where
"alkyl" has been defined previously.
[00164] As used herein, a "carbamoyl" group refers to a group having the structure -O-CO-NRXRY or -NRX-CO-O-RZ wherein Rx and Rγ have been defined above and R can be aliphatic, aryl, araliphatic, heterocycloaliphatic, heteroaryl, or heteroaraliphatic.
[00165] As used herein, a "carboxy" group refers to -COOH, -COORX, -OC(O)H,
-OC(O)RX when used as a terminal group; or -OC(O)- or -C(O)O- when used as an internal group.
[00166] As used herein, a "haloaliphatic" group refers to an aliphatic group substituted with 1, 2, or 3 halogen. For instance, the term haloalkyl includes the group -CF3.
[00167] As used herein, a "mercapto" group refers to -SH.
[00168] As used herein, a "sulfo" group refers to -SO3H or -SO3RX when used terminally or -S(O)3- when used internally.
[00169] As used herein, a "sulf amide" group refers to the structure -NRX-S(O)2-
NRYRZ when used terminally and -NRX-S(O)2-NRY- when used internally, wherein Rx, Rγ, and R have been defined above.
[00170] As used herein, a "sulfamoyl" group refers to the structure -S(O)2-NRXRY or -NRX-S (O)2-R2 when used terminally; or -S(O)2-NRX- or -NRX -S(O)2- when used internally, wherein Rx, Rγ, and Rz are defined above. i [00171] As used herein a "sulfanyl" group refers to -S-Rx when used terminally and -S- when used internally, wherein Rx has been defined above. Examples of sulfanyls include alkylsulfanyl. [00172] As used herein a "sulfinyl" group refers to -S(O)-RX when used terminally and -S(O)- when used internally, wherein Rx has been defined above.
[00173] As used herein, a "sulfonyl" group refers to-S(O)2-Rx when used terminally and -S(O)2- when used internally, wherein R has been defined above.
[00174] As used herein, a "sulfoxy" group refers to -O-SO-RX or -SO-O-RX, when used terminally and -0-S(O)- or -S(O)-O- when used internally, where R has been defined above.
[00175] As used herein, a "halogen" or "halo" group refers to fluorine, chlorine, bromine or iodine.
[00176] As used herein, an "alkoxycarbonyl," which is encompassed by the term carboxy, used alone or in connection with another group refers to a group such as alkyl-O-C(O)-
[00177] As used herein, an "alkoxyalkyl" refers to an alkyl group such as alkyl-O- alkyl-, wherein alkyl has been defined above.
[00178] As used herein, a "carbonyl" refer to -C(O)-.
[00179] As used herein, an "oxo" refers to =0.
[00180] As used herein, an "aminoalkyl" refers to the structure (Rx RY)N-alkyl-.
[00181] As used herein, a "cyanoalkyl" refers to the structure (NC)-alkyl-.
[00182] As used herein, a "urea" group refers to the structure -NRX-CO-NRYRZ and a "thiourea" group refers to the structure -NRX-CS-NRYRZ when used terminally and -NRX- CO-NRY- or -NRX-CS-NRY- when used internally, wherein Rx, Rγ, and Rz have been defined above.
[00183] As used herein, a "guanidino" group refers to the structure -N=C(N (R
RY))N(RXRY) wherein Rx and Rγ have been defined above.
[00184] As used herein, the term "amidino" group refers to the structure -
C=(NRX)N(RXRY) wherein Rx and Rγ have been defined above.
[00185] In general, the term "vicinal" refers to the placement of substituents on a group that includes two or more carbon atoms, wherein the substituents are attached to adjacent carbon atoms.
[00186] In general, the term "geminal" refers to the placement of substituents on a group that includes two or more carbon atoms,- wherein the substituents are attached to the same carbon atom.
[00187] The terms "terminally" and "internally" refer to the location of a group within a substituent. A group is terminal when the group is present at the end of the substituent not further bonded to the rest of the chemical structure. Carboxyalkyl, i.e., RxO(O)C-alkyl is an example of a carboxy group used terminally. A group is internal when the group is present in the middle of a substituent to at the end of the substituent bound to the rest of the chemical structure. Alkylcarboxy (e.g., alkyl-C(O)O- or alkyl-OC(O)-) and alkylcarboxyaryl (e.g., alkyl- C(O)O-aryl- or alkyl-O(CO)-aryl-) are examples of carboxy groups used internally.
[00188] As used herein, the term "amidino" group refers to the structure
-C=(NRX)N(RXRY) wherein Rx and Rγhave been defined above.
[00189] As used herein, "cyclic group" includes mono-, bi-, and tri-cyclic ring systems including cycloaliphatic, heterocycloaliphatic, aryl, or heteroaryl, each of which has been previously defined.
[00190] As used herein, a "bridged bicyclic ring system" refers to a bicyclic heterocyclicalipahtic ring system or bicyclic cycloaliphatic ring system in which the rings are bridged. Examples of bridged bicyclic ring systems include, but are not limited to, adamantanyl, norbornanyl, bicyclo[3.2.1]octyl, bicyclo[2.2.2]octyl, bicyclo[3.3.1]nonyl, bicyclo[3.2.3]nonyl, 2-oxa-bicyclo[2.2.2]octyl, l-aza-bicyclo[2.2.2]octyl, 3-aza- bicyclo[3.2.1]octyl, and 2,6-dioxa-tricyclo[3.3.1.03,7]nonyl. A bridged bicyclic ring system can be optionally substituted with one or more substituents such as alkyl (including carboxyalkyl, hydroxyalkyl, and haloalkyl such as trifluoromethyl), alkenyl, alkynyl, cycloalkyl, (cycloalkyl)alkyl, heterocycloalkyl, (heterocycloalkyl)alkyl, aryl, heteroaryl, alkoxy, cycloalkyloxy, heterocycloalkyloxy, aryloxy, heteroaryloxy, aralkyloxy, heteroaralkyloxy, aroyl, heteroaroyl, nitro, carboxy, alkoxycarbonyl, alkylcarbonyloxy, aminocarbonyl, alkylcarbonylamino, cycloalkylcarbonylamino, (cycloalkylalkyl)carbonylamino, arylcarbonylamino, aralkylcarbonylamino, (heterocycloalkyl)carbonylamino, (heterocycloalkylalkyl)carbonylamino, heteroarylcarbonylamino, heteroaralkylcarbonylamino, cyano, halo, hydroxy, acyl, mercapto, alkylsulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl.
[00191] As used herein, an "aliphatic chain" refers to a branched or straight aliphatic group (e.g., alkyl groups, alkenyl groups, or alkynyl groups). A straight aliphatic chain has the structure -[CH2]V-, where v is 1-6. A branched aliphatic chain is a straight aliphatic chain that is substituted with one or more aliphatic groups. A branched aliphatic chain has the structure -[CHQ]V- where Q is hydrogen or an aliphatic group; however, Q shall be an aliphatic group in at least one instance. The term aliphatic chain includes alkyl chains, alkenyl chains, and alkynyl chains, where alkyl, alkenyl, and alkynyl are defined above.
[00192] The phrase "optionally substituted" is used interchangeably with the phrase "substituted or unsubstituted." As described herein, compounds of the invention can optionally be substituted with one or more substituents, such as are illustrated generally above, or as exemplified by particular classes, subclasses, and species of the invention. As described herein, the variables R1, R2, R3, and R4, and other variables contained therein formulae I encompass specific groups, such as alkyl and aryl. Unless otherwise noted, each of the specific groups for the variables Ri, R2, R3, and R4, and other variables contained therein can be optionally substituted with one or more substituents described herein. Each substituent of a specific group is further optionally substituted with one to three of halo, cyano, oxoalkoxy, hydroxy, amino, nitro, aryl, haloalkyl, and alkyl. For instance, an alkyl group can be substituted with alkylsulfanyl and the alkylsulfanyl can be optionally substituted with one to three of halo, cyano, oxoalkoxy, hydroxy, amino, nitro, aryl, haloalkyl, and alkyl. As an additional example, the cycloalkyl portion of a (cycloalkyl)carbonylamino can be optionally substituted with one to three of halo, cyano, alkoxy, hydroxy, nitro, haloalkyl, and alkyl. When two alkoxy groups are bound to the same atom or adjacent atoms, the two alkoxy groups can form a ring together with the atom(s) to which they are bound.
[00193] In general, the term "substituted," whether preceded by the term
"optionally" or not, refers to the replacement of hydrogen radicals in a given structure with the radical of a specified substituent. Specific substituents are described above in the definitions and below in the description of compounds and examples thereof. Unless otherwise indicated, an optionally substituted group can have a substituent at each substitutable position of the group, and when more than one position in any given structure can be substituted with more than one substituent selected from a specified group, the substituent can be either the same or different at every position. A ring substituent, such as a heterocycloalkyl, can be bound to another ring, such as a cycloalkyl, to form a spiro-bicyclic ring system, e.g., both rings share one common atom. As one of ordinary skill in the art will recognize, combinations of substituents envisioned by this invention are those combinations that result in the formation of stable or chemically feasible compounds.
[00194] The phrase "up to", as used herein, refers to zero or any integer number that is equal or less than the number following the phrase. For example, "up to 3" means any one of 0, 1, 2, and 3. [00195] The phrase "stable or chemically feasible," as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and preferably their recovery, purification, and use for one or more of the purposes disclosed herein. In some embodiments, a stable compound or chemically feasible compound is one that is not substantially altered when kept at a temperature of 40° C or less, in the absence of moisture or other chemically reactive conditions, for at least a week.
[00196] As used herein, an effective amount is defined as the amount required to confer a therapeutic effect on the treated patient, and is typically determined based on age, surface area, weight, and condition of the patient. The interrelationship of dosages for animals and humans (based on milligrams per meter squared of body surface) is described by Freireich et al., Cancer Chemother. Rep., 50: 219 (1966). Body surface area may be approximately determined from height and weight of the patient. See, e.g., Scientific Tables, Geigy Pharmaceuticals, Ardsley, New York, 537 (1970). As used herein, "patient" refers to a mammal, including a human.
[00197] Unless otherwise stated, structures depicted herein are also meant to include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure; for example, the R and S configurations for each asymmetric center, (Z) and (E) double bond isomers, and (Z) and (E) conformational isomers. Therefore, single stereochemical isomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the invention. Unless otherwise stated, all tautomeric forms of the compounds of the invention are within the scope of the invention. Additionally, unless otherwise stated, structures depicted herein are also meant to include compounds that differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of hydrogen by deuterium or tritium, or the replacement of a carbon by a 1 C- or 14C~enriched carbon are within the scope of this invention. Such compounds are useful, for example, as analytical tools or probes in biological assays.
COMPOUNDS
[00198] Compounds of the present invention are useful modulators of ABC transporters and are useful in the treatment of ABC transport mediated diseases.
A. Generic Compounds
[00199] The present invention includes a compound of formula (I),
Figure imgf000023_0001
(I) or a pharmaceutically acceptable salt thereof, wherein:
Each R1 is an optionally substituted C1-6 aliphatic, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted C3-io cycloaliphatic, an optionally substituted 3 to 10 membered heterocycloaliphatic, carboxy [e.g., hydroxycarbonyl or alkoxycarbonyl], amido [e.g., aminocarbonyl], amino, halo, or hydroxy; provided that at least one R1 is an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl attached to the 5- or 6- position of the pyridyl ring;
Each R2 is hydrogen, an optionally substituted C1-6 aliphatic, an optionally substituted C3-6 cycloaliphatic, an optionally substituted phenyl, or an optionally substituted heteroaryl;
Each R3 and R'3 together with the carbon atom to which they are attached form an optionally substituted C3-7 cycloaliphatic or an optionally substituted heterocycloaliphatic;
Each R4 is an optionally substituted aryl or an optionally substituted heteroaryl; and
Each n is 1, 2, 3 or 4.
[00200] In another aspect, the present invention includes compounds of formula
(T):
Figure imgf000023_0002
or a pharmaceutically acceptable salt thereof, wherein: one of G1 and G2 is a nitrogen, and the other is a carbon; and
R1, R2, R3, R'3, R4, and n are defined above.
Specific Embodiments
A. Substituent R1
[00201] Each R1 is independently an optionally substituted C1-6 aliphatic, an optionally substituted aryϊ, an optionally substituted heteroaryl, an optionally substituted Cs-1O membered cycloaliphatic, an optionally substituted 3 to 10 membered heterocycloaliphatic, carboxy [e.g., hydroxycarbonyl or alkoxycarbonyl], amido [e.g., aminocarbonyl], amino, halo, or hydroxy.
[00202] In some embodiments, one R1 is an optionally substituted C1-6 aliphatic.
In several examples, one R1 is an optionally substituted C1-S alkyl, an optionally substituted C2-6 alkenyl, or an optionally substituted C2-6 alkynyl. In several examples, one Ri is Ci-6 alkyl, C2-6 alkenyl, or C2-6 alkynyl.
[00203] In several embodiments, one R1 is an aryl or heteroaryl with 1, 2, or 3 substituents. In several examples, one R1 is a monocyclic aryl or heteroaryl. In several embodiments, R1 is an aryl or heteroaryl with 1, 2, or 3 substituents. In several examples, Ri is a monocyclic aryl or heteroaryl.
[00204] In several embodiments, at least one Ri is an optionally substituted aryl or an optionally substituted heteroaryl and R] is bonded to the core structure at the 6 position on the pyridine ring.
[00205] In several embodiments, at least one Ri is an optionally substituted aryl or an optionally substituted heteroaryl and R1 is bonded to the core structure at the 5 position on the pyridine ring.
[00206] In several embodiments, one R1 is phenyl with up to 3 substituents. In several embodiments, R1 is phenyl with up to 3 substituents.
[00207] In several embodiments, one Ri is a heteroaryl ring with up to 3 substituents. In certain embodiments, one Ri is a monocyclic heteroaryl ring with up to 3 substituents. In other embodiments, one Ri is a bicyclic heteroaryl ring with up to 3 substituents. In several embodiments, R1 is a heteroaryl ring with up to 3 substituents. In certain embodiments, R1 is a monocyclic heteroaryl ring with up to 3 substituents. In other embodiments, R1 is a bicyclic heteroaryl ring with up to 3 substituents.
[00208] In several embodiments, one Ri is carboxy [e.g., hydroxycarbonyl or alkoxycarbonyl]. Or, one Ri is amido [e.g., aminocarbonyl]. Or, one Ri is amino. Or, is halo. Or, is cyano. Or, hydroxyl.
[00209] In some embodiments, R1 is hydrogen, methyl, ethyl, i-propyl, t-butyl, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, allyl, F, Cl, methoxy, ethoxy, i-propoxy, t- butoxy, CF3, OCF3, CN, hydroxyl, or amino. In several examples, R1 is hydrogen, methyl, methoxy, F, CF3 or OCF3. In several examples, R1 can be hydrogen. Or, R1 can be methyl. Or, R1 can be CF3. Or, R1 can be methoxy.
[00210] In several embodiments, R1 is substituted with no more than three substituents selected from halo, oxo, or optionally substituted aliphatic, cycloaliphatic, heterocycloaliphatic, amino [e.g., (aliphatic)amino], amido [e.g., aminocarbonyl, ((aliphatic)amino)carbonyl, and ((aliphatic)2amino)carbonyl3, carboxy [e.g., alkoxycarbonyl and hydroxycarbonyl], sulfamoyl [e.g., aminosulfonyl, ((aliphatic)2amino)sulfonyl, ((cycloaliphatic)aliphatic)aminosulfonyl, and ((cycloaliphatic)amino)sulfonyl], cyano, alkoxy, aryl, heteroaryl [e.g., monocyclic heteroaryl and bicycloheteroaryl], sulfonyl [e.g., aliphaticsulfonyl or (heterocycloaliphatic)sulfonyl], sulfinyl [e.g., aliphaticsulfinyl], aroyl, heteroaroyl, or heterocycloaliphaticcarbonyl.
[00211] In several embodiments, R1 is substituted with halo. Examples of R1 substituents include F, Cl, and Br. In several examples, R1 is substituted with F.
[00212] In several embodiments, Ri is substituted with an optionally substituted aliphatic. Examples of Ri substituents include optionally substituted alkoxyaliphatic, heterocycloaliphatic, aminoalkyl, hydroxyalkyl, (heterocycloalkytyaliphatic, alkylsulfonylaliphatic, alkylsulfonylaminoaliphatic, alkylcarbonylaminoaliphatic, alkylaminoaliphatic, or alkylcarbonylaliphatic.
[00213] In several embodiments, R1 is substituted with an optionally substituted amino. Examples of R1 substituents include aliphaticcarbonylamino, aliphaticamino, arylamino, or aliphaticsulfonylamino.
[00214] In several embodiments, R1 is substituted with a sulfonyl. Examples of
Ri substituents include heterocycloaliphaticsulfonyl, aliphatic sulfonyl, aliphaticaminosulfonyl, aminosulfonyl, aliphaticcarbonylaminosulfonyl, alkoxyalkylheterocycloalkylsulfonyl, alkylheterocycloalkylsulfonyl, alkylaminosulfonyl, cycloalkylaminosulfonyl, (heterocycloalkytyalkylaminosulfonyl, and heterocycloalkylsulfonyl.
[00215] In several embodiments, R1 is substituted with carboxy. Examples of R1 substituents include alkoxycarbonyl and hydroxycarbonyl.
[00216] In several embodiments R1 is substituted with amido. Examples Of R1 substituents include alkylaminocarbonyl, aminocarbonyl, ((aliphatic)2amino)carbonyl, and [((aliphatic)aminoaliphatic)amino]carbonyl.
[00217] In several embodiments, R1 is substituted with carbonyl. Examples Of R1 substituents include arylcaϊbonyl, cycloaliphaticcarbonyl, heterocycloaliphaticcarbonyl, and heteroarylcarbonyl.
[00218] In some embodiments, R1 is hydrogen. In some embodiments, R1 is -
ZAR5, wherein each ZA is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZA are optionally and independently replaced by -CO-, -CS-, -C0NRA-, -CONRANRA-, -CO2-, -OCO-, -NRAC02-, -O-, - NRACONRA-, -OCONRA-, -NRANRA-, -NRAC0-, -S-, -SO-, -SO2-, -NRA-, -SO2NRA-, - NRASO2-, or -NRASO2NRA-. Each R5 is independently RA, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3. Each RA is independently a C1-8 aliphatic group, a cycloaliphatic, a heterocycloaliphatic, an aryl, or a heteroaryl, each of which is optionally substituted with 1, 2, or 3 of RD. Each RD is -ZDR9, wherein each ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -C0NRE-, -C0NRENRE-, -CO2-, -OCO-, -NRECO2-, -0-, -NRECONRE-, -OCONRE-, -NRENRE-, -NRBC0-, -S-, -SO-, -SO2-, -NRB-, - S02NRE-, -NRES02-, or -NRES02NRE-. Each R9 is independently RE, halo, -OH, -NH2, -NO2, - CN, -CF3, or -OCF3. Each RE is independently hydrogen, an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00219] In some embodiments, each RD is independently -Z0R9; wherein each ZD can independently be a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -O-, - NHC(O)-, -C(0)NRE-, -SO2-, -NHSO2-, -NHC(O)-, -NRESO2-, -SO2NH-, -SO2NRE-, -NH-, or - C(O)O-. In some embodiments, one carbon unit of ZD is replaced by -0-. Or, by -NHC(O)-. Or, by -C(0)NRE-. Or, by -SO2-. Or, by -NHSO2-. Or, by -NHC(O)-. Or, by -SO-. Or, by - NRESO2-. Or, by -SO2NH-. Or, by -S02NRE-. Or, by -NH-. Or, by -C(O)O-.
[00220] In some embodiments, R9 is hydrogen. In some embodiments, R9 is independently an optionally substituted aliphatic. In some embodiments, R9 is an optionally substituted cycloaliphatic. Or, is an optionally substituted heterocycloaliphatic. Or, is an optionally substituted aryl. Or, is an optionally substituted heteroaryl. Or, halo.
[00221] In some embodiments, one R1 is aryl or heteroaryl, each optionally substituted with 1, 2, or 3 of RD, wherein RD is defined above.
[00222] In several embodiments, one R1 is carboxy [e.g., hydroxycarbonyl or alkoxycarbonyl]. Or, one R1 is amido [e.g., aminocarbonyl]. Or, one R1 is amino. Or, is halo. P> if"" T / J 11C f| jC / LL "3 p O Q
Or, is cyano. Or, hydroxyl.
[00223] In some embodiments, one R1 that is attached to 5- or 6- position of the pyridyl ring is aryl or heteroaryl, each optionally substituted with 1, 2, or 3 of RD, wherein RD is defined above. In some embodiments, the one R1 attached to the 5- or 6- postion of the pyridyl ring is phenyl optionally substituted with 1, 2, or 3 of RD, wherein RD is defined above. In some embodiments, the one Ri attached to the 5- or 6- position of the pyridyl ring is heteroaryl optionally substituted with 1, 2, or 3 of RD. In several embodiments, the one Ri attached to the 5- or 6- position of the pyridyl ring is 5 or 6 membered heteroaryl having 1, 2, or 3 heteroatom independently selected from the group consisting of oxygen, nitrogen and sulfur. In other embodiments, the 5 or 6 membered heteroaryl is substituted with 1 RD.
[00224] In some embodiments, one Ri attached to the 5- or 6- position of the pyridyl ring is a phenyl substituted with 1 RD. In some embodiments, one R1 attached to the 5- or 6- position of the pyridyl ring is a phenyl substituted with 2 RD. In some embodiments, one Ri attached to the 5- or 6- position of the pyridyl ring is a phenyl substituted with 3 RD.
[00225] In several embodiments, R1 is:
Figure imgf000027_0001
(Z-I), or (Z-2). wherein
Wi is -C(O)-, -SO2-, or -CH2-;
D is H, hydroxyl, or an optionally substituted group selected from aliphatic, cycloaliphatic, alkoxy, and amino; and RD is defined above.
[00226] In several embodiments, W1 is -C(O)-. Or, W] is -SO2-. Or, Wi is -CH2-.
[00227] In several embodiments, D is OH. Or, D is an optionally substituted Ci-6 aliphatic or an optionally substituted C3-C8 cycloaliphatic. Or, D is an optionally substituted alkoxy. Or, D is an optionally substituted amino.
[00228] In several examples, D is
Figure imgf000027_0002
P £.:: 1 VJ U B
Figure imgf000028_0001
and B is independently H, an optionally substituted C1-6 aliphatic, an optionally substituted C3-C8 cycloaliphatic, or
A and B, taken together, form an optionally substituted 3-7 membered heterόcycloaliphatic ring.
[00229] In several embodiments, A is H and B is an optionally substituted Ci-6 aliphatic. In several embodiments, B is substituted with 1, 2, or 3 substituents. Or, both, A and B, are H. Exemplary substituents include oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, dialkyamino, or an optionally substituted group selected from cycloaliphatic, heterocycloaliphatic, aryl, and heteroaryl.
[00230] In several embodiments, A is H and B is an optionally substituted C1-6 aliphatic. Or, both, A and B, are H. Exemplary substituents include oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, and an optionally substituted heterocycloaliphatic.
[00231] In several embodiments, B is C1-6 alkyl, optionally substituted with oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, or an optionally substituted group selected from cycloaliphatic, heterocycloaliphatic, aryl, and heteroaryl. In several embodiments, B is substituted with oxo, Ci-6 alkyl, hydroxy, hydroxy-(C1-e)alkyl, (C1-6)alkoxy, (C1-^aIkOXy(C1- 6)alkyl, C3_8 cycloaliphatic, 3-8 membered heterocycloaliphatic, phenyl, and 5-10 membered heteroaryl. In one example, B is Ci-6 alkyl substituted with optionally substituted phenyl.
[00232] In several embodiments, A and B, taken together, form an optionally substituted 3-7 membered heterocycloaliphatic ring. In several examples, the heterocycloaliphatic ring is optionally substituted with 1, 2, or 3 substituents. Exemplary such rings include optionally substituted pyrrolidinyl, piperidinyl, morpholinyl, and piperazinyl. Exemplary substituents on such rings include halo, oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, acyl (e.g., alkylcarbonyl), amino, amido, and carboxy. In some embodiments, the substituent is halo, oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, amino, amido, or carboxy.
[00233] In several embodiments, RD is hydrogen, halo, or an optionally substituted group selected from aliphatic, cycloaliphatic, amino, hydroxy, alkoxy, carboxy, amido, carbonyl, cyano, aryl, or heteroaryl. In several examples, RD is hydrogen, halo, an optionally substituted Ci-6 aliphatic, or an optionally substituted alkoxy. In several examples, RD is hydrogen, F, Cl, an optionally substituted Ci-6 alkyl, or an optionally substituted -0(Ci-6 alkyl). Examples of RD include hydrogen, F, Cl, methyl, ethyl, /-propyl, ϊ-butyl, -OMe, -OEt, i- propoxy, t-butoxy, CF3, or -OCF3. In some examples, RDis hydrogen, F, methyl, methoxy, CF3, P C T ./" Ii S Q IEL/" s+3 F? H cj n n D or -OCF3. R can be hydrogen. R can be F. Ru can be methyl. R can be methoxy.
[00234] In several embodiments, R1 is:
Figure imgf000029_0001
(Z); wherein:
W1 is -C(O)-, -SO2-, or -CH2-;
Each of A and B is independently H, an optionally substituted C1-6 aliphatic, an optionally substituted C3-C8 cycloaliphatic; or
A and B, taken together, form an optionally substituted 3-7 membered heterocycloaliphatic ring.
[00235] In some embodiments, one R1 that is attached to the 5- or 6- position of the pyridyl ring is cycloaliphatic or heterocycloaliphatic, each optionally substituted with 1, 2, or 3 of RD ; wherein RD is -Z0R9; wherein each ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of Z are optionally and independently replaced by -CO-, -CS-, -C0NRE-, -C0NRENRE-, -CO2-, -OCO-, -NREC02-, -O-, -NRECONRE-, -0C0NRE-, -NRENRE-, -NRECO-, -S-, -SO-, -SO2-, -NRE-, - SO2NR1S -NR13SO2-, or -NRES02NRE-; each R9 is independently RE, halo, -OH, -NH2, -NO2, - CN, -CF3, or -OCF3; and each RE is independently hydrogen, an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00236] In several examples, one R1 that is attached to the 5- or 6- position of the pyridyl ring is an optionally substituted C3-C8 cycloaliphatic.
[00237] In some embodiments, one R1 that is attached to the 5- or 6- position of the pyridyl ring is an optionally substituted C3-C8 cycloalkyl or an optionally substituted C3-C8 cycloalkenyl.
[00238] In several embodiments, one R1 that is attached to the 5- or 6- position of the pyridyl ring is C3-C8 cycloalkyl or C3-C8 cycloalkenyl. Examples of cycloalkyl and cycloalkenyl include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclopentenyl,cyclohexenyl,and cycloheptenyl.
[00239] In some embodiments, Rl is:
Figure imgf000030_0001
Figure imgf000031_0001
Figure imgf000031_0002
Figure imgf000031_0003
Figure imgf000031_0004
Figure imgf000031_0005
Figure imgf000032_0001
Figure imgf000032_0002
Figure imgf000032_0003
Figure imgf000032_0004
Figure imgf000032_0005
Figure imgf000033_0001
Figure imgf000033_0002
Figure imgf000033_0004
Figure imgf000034_0001
Figure imgf000034_0002
Figure imgf000034_0003
Figure imgf000034_0004
Figure imgf000034_0005
Figure imgf000034_0006
Figure imgf000035_0001
Figure imgf000035_0002
Figure imgf000035_0003
Figure imgf000036_0001
Figure imgf000036_0002
Figure imgf000036_0003
Figure imgf000036_0004
Figure imgf000036_0005
Figure imgf000036_0006
Figure imgf000037_0001
Figure imgf000037_0002
Figure imgf000037_0003
Figure imgf000037_0004
Figure imgf000038_0001
Figure imgf000038_0002
Figure imgf000038_0003
Figure imgf000038_0004
Figure imgf000039_0001
Figure imgf000039_0002
Figure imgf000039_0003
Figure imgf000039_0004
Figure imgf000039_0005
Figure imgf000040_0001
, or
[00240] In several examples, R1 is one selected from:
Figure imgf000040_0002
Figure imgf000041_0001
Figure imgf000042_0001
Figure imgf000043_0001
Figure imgf000044_0001
Figure imgf000045_0001
B. Substituent R2
[00241] Each R2 can be hydrogen. Each R2 can be an optionally substituted group selected from C1-6 aliphatic, C3-6 cycloaliphatic, phenyl, and heteroaryl.
[00242] In several embodiments, R2 is a C1-6 aliphatic optionally substituted with
1, 2, or 3 halo, C1-2 aliphatic, or alkoxy. In several examples, R2 can be substituted methyl, ethyl, propyl, or butyl. In several examples, R2 can be methyl, ethyl, propyl, or butyl.
[00243] In several embodiments, R2 is hydrogen.
C. Substituents R3 and R'3
[00244] Each R3 and R'3 together -with the carbon atom to which they are attached form a C3./7 cycloaliphatic or a heterocycloaliphatic, each of which is optionally substituted with 1, 2, or 3 substituents.
[00245] In several embodiments, R3 and R'3 together with the carbon atom to which they are attached form a C3-7 cycloaliphatic or a C3-7 heterocycloaliphatic, each of which is optionally substituted with 1, 2, or 3 of -ZBR7, wherein each ZB is independently a bond, or an optionally substituted branched or straight C1-4 aliphatic chain wherein up to two carbon units of ZB are optionally and independently replaced by -CO-, -CS-, -CONRB-, -CONRBNRB-, -CO2-, - OCO-, -NR13CO2-, -O-, -NRBCONRB-, -OCONR5-, -NRBNRB-, -NR8CO-, -S-, -SO-, -SO2-, - NRB-, -SO2NRB -, -NRBSO2-, or -NRBS02NRBs each R7 is independently RB, halo, -OH, -NH2, - NO2, -CN, -CF3, or -OCF3; and each RB is independently hydrogen, an optionally substituted C1- 8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00246] In several embodiments, R3 and R'3 together with the carbon atom to which they are attached form a 3, 4, 5, or 6 membered cycloaliphatic that is optionally substituted with 1, 2, or 3 substituents. In several examples, R3, R3, and the carbon atom to which they are attached form an optionally substituted cyclopropyl group. In several alternative examples, R3, R'3, and the carbon atom to which they are attached form an optionally substituted cyclobutyl group. In several other examples, R3, R'3, and the carbon atom to which they are attached form an optionally substituted cyclopentyl group. In other examples, R3, R'3, and the carbon atom to which they are attached form an optionally substituted cyclohexyl group. In more examples, R3 and R3 together with the carbon atom to which they are attached form an unsubstituted cyclopropyl.
[00247] In several embodiments, R3 and R3 together with the carbon atom to which they are attached form a 5, 6, or 7 membered optionally substituted heterocycloaliphatic. In other examples, R3, R'3, and the carbon atom to which they are attached form an optionally substituted tetrahydropyranyl group.
[00248] In some embodiments, R3 and R'3 together with the carbon atom to which they are attached form an unsubstituted C3-7 cycloaliphatic or an unsubstituted heterocycloaliphatic. In several examples, R3 and R3 together with the carbon atom to which they are attached form an unsubstituted cyclopropyl, an unsubstituted cyclopentyl, or an unsubstituted cyclohexyl.
D. Substituent R4
[00249] Each R4 is independently an optionally substituted aryl or an optionally substituted heteroaryl.
[00250] In several embodiments, R4 is an aryl having 6 to 10 members (e.g., 7 to
10 members) optionally substituted with 1, 2, or 3 substituents. Examples of R4 include optionally substituted benzene, naphthalene, or indene. Or, examples of R4 can be optionally substituted phenyl, optionally substituted naphthyl, or optionally substituted indenyl.
[00251] In several embodiments, R4 is an optionally substituted heteroaryl.
Examples of R4 include monocyclic and bicyclic heteroaryl, such a benzofused ring system in which the phenyl is fused with one or two 4-8 membered heterocycloaliphatic groups.
[00252] In some embodiments, R4 is an aryl or heteroaryl, each optionally substituted with 1, 2, or 3 of -Z0R8. In some embodiments, R4 is an aryl optionally substituted with 1, 2, or 3 of -Z0R8. In some embodiments, R4 is phenyl optionally substituted with 1, 2, or 3 of -Z0R8. Or, R4 is a heteroaryl optionally substituted with 1, 2, or 3 of -Z0R8. Each Z° is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of Z° are optionally and independently replaced by -CO-, -CS-, - CONR0-, -CONR0NR0-, -CO2-, -OCO-, -NR0CO2-, -O-, -NR0CONR0-, -OCONR0-, -NR0NR0- , -NR0CO-, -S-, -SO-, -SO2-, -NR0-, -SO2NR0-, -NR0SO2-, or -NR0SO2NR0-. Each R8 is independently Rc, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3. Each Rc is independently hydrogen, an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00253] In some embodiments, two occurrences of -Z0R8, taken together with carbons to which they are attached, form a 4-8 membered saturated, partially saturated, or aromatic ring with up to 3 ring atoms independently selected from the group consisting of O, NH, NRC, and S; wherein Rc is defined herein.
[00254] In several embodiments, R4 is one selected from
Figure imgf000048_0001
Figure imgf000048_0002
Figure imgf000048_0003
E. Exemplary Compound Families
[00255] In several embodiments, R1 is an optionally substituted cyclic group that is attached to the core structure at the 5 or 6 position of the pyridine ring.
[00256] In several examples, Ri is an optionally substituted aryl that is attached to the 5 position of the pyridine ring. In other examples, R1 is an optionally substituted aryl that is attached to the 6 position of the pyridine ring.
[00257] In more examples, Rj is an optionally substituted heteroaryl that is attached to the 5 position of the pyridine ring. In still other examples, R1 is an optionally substituted heteroaryl that is attached to the 6 position of the pyridine ring.
[00258] In other embodiments, R1 is an optionally substituted cycloaliphatic or an optionally substituted heterocycloaliphatic that is attached to the pyridine ring at the 5 or 6 position.
[00259] Accordingly, another aspect of the present invention provides compounds of formula (II):
Figure imgf000049_0001
(H) or a pharmaceutically acceptable salt thereof, wherein R1, R2, R3, R3, and R4 are defined in formula I.
[00260] In some embodiments, each R1 is aryl or heteroaryl optionally substituted with 1, 2, or 3 of RD, wherein RD is -Z0Rg, wherein each ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -CONRE-, -CONRENRE-, -CO2-, - OCO-, -NRECO2-, -O-, -NRECONRE-, -OCONRE-, -NRENRE-, -NRECO-, -S-, -SO-, -SO2-, - NRE-, -SO2NRE-, -NRESO2-, or -NRESO2NRE-; each R9 is independently RE, halo, -OH, -NH2, - NO2, -CN, -CF3, or -OCF3; each R is independently hydrogen, an optionally substituted Cj-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00261] In some embodiment, each R1 is cycloaliphatic or heterocycloaliphatic optionally substituted with 1, 2, or 3 of RD; wherein RD is defined above.
[00262] Another aspect of the present invention provides compounds of formula
(HI):
Figure imgf000049_0002
(HI) or a pharmaceutically acceptable salt thereof, wherein R1, R2, R3, R3, and R4 are defined in formula I.
[00263] In some embodiments, each R1 is aryl or heteroaryl optionally substituted with 1, 2, or 3 of RD, wherein RD is -Z0Rg, wherein each ZD is independently a bond or an optionally substituted branched or straight Ci-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -CONRE-, -C0NRENRE-, -CO2-, - OCO-, -NRECO2-, -O-, -NREC0NRE-, -OCONRE-, -NRENRE-, -NREC0-, -S-, -SO-, -SO2-, - NRE-, -SO2NRE-, -NRESO2-, or -NRESO2NRE-; each R9 is independently RE, halo, -OH, -NH2, - NO2, -CN, -CF3, or -OCF3; each RE is independently hydrogen, an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00264] In some embodiments, each R1 is cycloaliphatic or heterocycloaliphatic optionally substituted with 1, 2, or 3 of RD; wherein RD is defined above.
[00265] In another aspect, the present invention includes compounds of formula
(IV):
Figure imgf000050_0001
(IV) or a pharmaceutically acceptable salt thereof, wherein R2, R3, R'3, and R4 are defined in formula I.
[00266] RD is -Z0R9; wherein each ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -CONRE-, -CONRENRE-, -CO2-, -OCO-, -NREC02-, -O-, -NRECONRE-, -OCONRE-, -NRENRE-, -NRECO-, -S-, -SO-, -SO2-, -NRE-, - SO2NRE-, -NRESO2-, or -NRES02NRE-.
[00267] R9 is independently RE, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3.
[00268] Each RE is independently hydrogen, an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl. [00269] In several embodiments, ZD is independently a bond or is an optionally substituted branched or straight C1-6 aliphatic chain wherein one carbon unit of ZD is optionally replaced by -SO2-, -CONRE-, - NRESO2-, or -SO2NRE-. For example, ZD is an optionally substituted branched or straight C1-6 aliphatic chain wherein one carbon unit of ZD is optionally replaced by -SO2-. In other examples, R9 is an optionally substituted heteroaryl or an optionally substituted heterocycloaliphatic. In additional examples, R9 is an optionally substituted heterocycloaliphatic having 1-2 nitrogen atoms, and R9 attaches directly to -SO2- via a ring nitrogen.
[00270] In another aspect, the present invention includes compounds of formula
V-A or formula V-B:
Figure imgf000051_0001
V-A V-B or a pharmaceutically acceptable salt thereof, wherein:
T is an optionally substituted C1-2 aliphatic chain, wherein each of the carbon units is optionally and independently replaced by -CO-, -CS-, -COCO-, -SO2-, -B(OH)-, or -B(O(C1-6 alkyl))-;
Each of Ri' and Ri" is independently a bond or an optionally substituted Ci-6 aliphatic, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted 3 to 10 membered cycloaliphatic, an optionally substituted 3 to 10 membered heterocycloaliphatic, carboxy, amido, amino, halo, or hydroxy;
Rm is attached to carbon 3" or 4"; each RD1 and RD2 is -ZDR9, wherein each ZD is independently a bond or an optionally substituted branched or straight Ci-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -C0NRE-, -C0NRENRE-, -CO2-, -OCO-, -NREC02-, -O-, -NREC0NRE-, -0C0NRE-, -NRENRE-, -NREC0-, -S-, -SO-, -SO2-, -NRE-, - S02NRE-, -NRESO2-, or -NRES02NRE-;
R9 is independently RE, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3; or RD1 and RD2, taken together with atoms to which they are attached, form a 3-8 membered saturated, partially unsaturated, or aromatic ring with up to 3 ring members independently selected from the group consisting of O, NH, NR , and S; and each RE is independently hydrogen, an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
[00271] In some embodiments, T is an optionally substituted -CH2-. In some other embodiments, T is an optionally substituted -CH2CH2-.
[00272] In some embodiments, T is optionally substituted by -ZER10; wherein each ZE is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZB are optionally and independently replaced by -CO-, - CS-, -CONRF-, -CONRFNRF-, -CO2-, -OCO-, -NRFCO2-, -O-, -NRFCONRF-, -OCONRF-, - NRFNRF-, -NRFCO-, -S-, -SO-, -SO2-, -NRF-, -SO2NRF-, -NRFSO2-, or -NRFSO2NRF-; R10 is independently RF, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3; each RF is independently hydrogen, an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl. In one example, ZE is -0-.
[00273] In some embodiments, R1Q can be an optionally substituted C1-6 alkyl, an optionally substituted C2-6 alkenyl, an optionally substituted C3-7 cycloaliphatic, or an optionally substituted C6-10 aryl. In one embodiment, R1O is methyl, ethyl, /-propyl, or /-butyl.
[00274] In some embodiments, up to two carbon units of T are optionally substituted by -CO-, -CS-, -B(OH)-, or -B(O(Ci-6 alkyl)-.
[00275] In some embodiments, T is selected from the group consisting of -CH2-, -
Figure imgf000052_0001
CH2-. Or5 T iS -CF2-. Or, T is -C(CH3)2-.
[00276] In some embodiments, each of R1' and R1" is hydrogen. In some embodiments, each Of R1' and R1" is independently -ZARs, wherein each ZA is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZA are optionally and independently replaced by -CO-, -CS-, -CONRA-, - CONRANRA-, -CO2-, -OCO-, -NRAC02-, -0-, -NRAC0NRA-, -0C0NRA-, -NRANRA-, - NRACO-, -S-, -SO-, -SO2-, -NRA-, -SO2NRA-, -NRAS02-, or -NRASO2NRA-. Each R5 is independently RA, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3. Each RA is independently an optionally substituted group selected from C1-8 aliphatic group, a cycloaliphatic, a heterocycloaliphatic, an aryl, and a heteroaryl.
[00277] In some embodiments, R1' is selected from the group consisting of H, C1-6 aliphatic, halo, CF3, CHF2, -0(C1-6 aliphatic), C3-C5 cycloalkyl, or C4-C6 heterocycloalkyl containing one oxygen atom. In some embodiments, R1' is selected from the group consisting of H, methyl, ethyl, i-propyl, t-butyl, F. Cl, CF3, CHF2, -OCH3, -OCH2CH3, -O-(z-propyl), or -O- (t-butyl). More preferably, R1 1 Is H. Or, R1' is methyl. Or, ethyl. Or5 CF3.
[00278] In some embodiments, R1" is selected from the group consisting of H, C1-
6 aliphatic, halo, CF3, CHF2, and -0(Ci-6 aliphatic). In some embodiments, R1" is selected from the group consisting of H5 methyl, ethyl, z-propyl, t-butyl, F. Cl, CF3, CHF2, -OCH3, - OCH2CH3, -O-(ι-propyl), or -O-(t-butyl). More preferably, R1" is H. Or, R1" is methyl. Or, ethyl. Or5 CF3.
[00279] In some embodiments, Rm is attached to carbon 3" or 4", and is -ZDR9, wherein each ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -C0NRE-, -CONRENRE-, -CO2-, -OCO-, -NR2CO2-, -O-, -NREC0NRE-, - 0C0NRE-5 -NRENRE-, -NREC0-, -S-, -SO-, -SO2-, -NRE-5 -SO2NRE-5 -NRESO2-5 or - NRESθ2NRE-. In yet some embodiments, ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein one carbon unit of ZD is optionally replaced by -CO-, -SO-, -SO2-, -COO-, -OCO-, -CONRE-, -NREC0-, NREC02-, -0-, -NR12SO2- , or -Sθ2NRE-. In some embodiments, one carbon unit of ZD is optionally replaced by -CO-. Or, by -SO-. Or, by -SO2-. Or, by -COO-. Or, by -OCO-. Or5 by -C0NRE-. Or, by -NRECO-. Or, by -NREC02-. Or, by -O-. Or, by -NRESO2-. Or, by -SO2NRE-.
[00280] In several embodiments, R9 is hydrogen, halo, -OH, -NH2, -CN, -CF3, -
OCF3, or an optionally substituted group selected from the group consisting of C1-6 aliphatic, C3- s cycloaliphatic, 3-8 membered heterocycloaliphatic, Cg-io aryl, and 5-10 membered heteroaryl. In several examples, R9 is hydrogen, F, Cl, -OH, -CN, -CF3, or -OCF3. In some embodiments, R9 is C1-6 aliphatic, C3-8 cycloaliphatic, 3-8 membered heterocycloaliphatic, Cg-io aryl, and 5-10 membered heteroaryl, each of which is optionally substituted by 1 or 2 substituents independently selected from the group consisting of RE, oxo, halo, -OH, -NRERB, -ORE, - COORE, and -CONRERE. In several examples, R9 is optionally substituted by 1 or 2 substituents independently selected from the group consisting of oxo, F, Cl, methyl, ethyl, i- propyl, ϊ-butyl, -CH2OH, -CH2CH2OH, -C(O)OH, -C(O)NH2, -CH2O(Ci-6 alkyl), - CH2CH2O(C1-6 alkyl), and -C(O)(Ci-6 alkyl).
[00281] In one embodiment, R9 is hydrogen. In some embodiments, R9 is selected from the group consisting of Ci-6 straight or branched alkyl or C2-(S straight or branched alkenyl; wherein said alkyl or alkenyl is optionally substituted by 1 or 2 substituents independently selected from the group consisting of RE, oxo, halo, -OH, -NRERE, -0RE, - COORE, and -CONRERE.
[00282] In other embodiments, R9 is C3-8 cycloaliphatic optionally substituted by
1 or 2 substituents independently selected from the group consisting of RB, oxo, halo, -OH, - NRERE, -ORE, -COORE, and -CONRERE. Examples of cycloaliphatic include but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl.
[00283] In yet other embodiments, R9 is a 3-8 membered heterocyclic with 1 or 2 heteroatoms independently selected from the group consisting of O, NH, NRE, and S; wherein said heterocyclic is optionally substituted by 1 or 2 substituents independently selected from the group RE, oxo, halo, -OH, -NRERE, -0RE, -COORE, and -CONRERE. Example of 3-8 membered heterocyclic include but are not limited to
Figure imgf000054_0001
[00284] In yet some other embodiments, R9 is an optionally substituted 5-8 membered heteroaryl with one or two ring atom independently selected from the group consisting of O, S, and NRE. Examples of 5-8 membered heteroaryl include but are not limited to
Figure imgf000054_0002
Figure imgf000055_0001
[00285] In some embodiments, RDI and RD2, taken together with carbons to which they are attached, form an optionally substituted 4-8 merαbered saturated, partially unsaturated, or aromatic ring with 0-2 ring atoms independently selected from the group consisting of O, NH, NRE, and S. Examples of RDI and RD2, taken together with phenyl containing carbon atoms 3" and 4", include but are not limited to
Figure imgf000055_0002
an
[00286] In some embodiments, RD2 is selected from the group consisting of H, RE, halo, -OH, -(CH2)rNRERE, -(CH2)r-ORE, -SO2-RE, -NRE-SO2~RE, -SO2NRERE, -C(O)RE, - C(O)ORE, -OC(O)ORE, -NREC(O)ORE ? and -C(O)NRERE; wherein r is 0, 1, or 2. In other embodiments, Rm is selected from the group consisting of H, Ci-6 aliphatic, halo, -CN, -NH2, - NH(C1-6 aliphatic), -N(Ci-6 aliphatic)2, -CH2-N( C1-6 aliphatic)2, -CH2-NH(C1-6 aliphatic), - CH2NH2, -OH, -0(Ci-6 aliphatic), -CH2OH, -CH2-O(Ci-6 aliphatic), -SO2( C1-6 aliphatic), -N( C1-6 aliphatic)-SO2(CV6 aliphatic), -NH-SO2(C1-6 aliphatic), -SO2NH2, -SO2NH(Ci-6 aliphatic), - SO2N( C1-6 aliphatic)2, -C(O)(C1-6 aliphatic), -C(O)O(Ci-6 aliphatic), -C(O)OH, -OC(O)O( C1-6 aliphatic), -NHC(O)(C1-6 aliphatic), -NHC(O)O(Ci-6 aliphatic), -N( C1-6 a]iphatic)C(O)O( C1-6 aliphatic), -C(O)NH2, and -C(O)N(C1-6 aliphatic)2. In several examples, RD2 is selected from the group consisting of H, Ci-6 aliphatic, halo, -CN, -NH2, -CH2NH2, -OH, -0(Ci-6 aliphatic), - CH2OH, -SO2( C1-6 aliphatic), -NH-SO2(C1-6 aliphatic), -C(O)O(Ci-6 aliphatic), -C(O)OH, - NHC(O)(C1-6 aliphatic), -C(O)NH2, -C(O)NH(C1-6 aliphatic), and -C(O)N(C1-6 aliphatic)2. For examples, RD2 is selected from the group consisting of H, methyl, ethyl, n-propyl, i-propyl, t- butyl, F, Cl, CN, -NH2, -CH2NH2, -OH, -OCH3, -O-ethyl, -O-(i-propyl), -O~(n-propyl), - CH2OH, -SO2CH3, -NH-SO2CH3, -C(O)OCH3, -C(O)OCH2CH3, -C(O)OH, -NHC(O)CH3, - C(O)NH2, and -C(O)N(CHs)2. In one embodiment, RD2 is hydrogen. In another embodiment,
R >Du2/ i ■s methyl. Or, R >Dω2 i •s ethyl. Or, R D^2 is R Or, R >Dυ2i i. s Cl. Or1 -OCH3.
[00287] In one embodiment, the present invention provides compounds of formula VI-A -i or formula VI-A-ii:
Figure imgf000056_0001
wherein T, Rm, Rm, and R1' are as defined above.
[00288] In one embodiment, T is -CH2-, -CF2-, or -C(CH3)2-.
[00289] In one embodiment, Ri' is selected from the group consisting of H, C1-6 aliphatic, halo, CF3, CHF2, -0(Cj-5 aliphatic), C3-C5 cycloalkyl, or C4-C6 heterocycloalkyl containing one oxygen atom. Exemplary embodiments include H, methyl, ethyl, i-propyl, t- butyl, F. Cl, CF3, CHF2, -OCH3, -OCH2CH3, -O-(i-ρropyl), -O-(t-butyl), cyclopropyl, or oxetanyl. More preferably, R1' is H. Or, R1' is methyl. Or, ethyl. Or, CF3. Or, oxetanyl.
[00290] In one embodiment, Rm is ZDR9, wherein ZD is selected from CONH,
NHCO, SO2NH, SO2N(Ci-6 alkyl), NHSO2, CH2NHSO2, CH2N(CH3)SO2, CH2NHCO, COO, SO2, or CO. In one embodiment, Rm is ZDR9, wherein ZD is selected from CONH, SO2NH, SO2N(C1-6 alkyl), CH2NHSO2, CH2N(CH3)SO2, CH2NHCO, COO, SO2, or CO.
[00291] In one embodiment, ZD is COO and R9 is H. In one embodiment, 2? is
COO and R9 is an optionally substituted straight or branched C1-6 aliphatic. In one embodiment, ZD is COO and R9 is an optionally substituted straight or branched Ci-^ alkyl. In one embodiment, ZD is COO and R9 is C1-6 alkyl. In one embodiment, ZD is COO and R9 is methyl.
[00292] In one embodiment, ZD is CONH and R9 is H. In one embodiment, ZD is
CONH and R9 is an optionally substituted straight or branched C1-6 aliphatic. In one embodiment, ZD is CONH and R9 is straight or branched C1-6 alkyl. In one embodiment, ZD is CONH and R9 is methyl. In one embodiment, ZD is CONH and R9 is an optionally substituted straight or branched C1-6 alkyl. In one embodiment, In one embodiment, ZD is CONH and R9 is 2-(dimethylamino)-ethyl. [00293] In some embodiments, ZD is CH2NHCO and R9 is an optionally substituted straight or branched C1-6 aliphatic or an optionally substituted alkoxy. In some embodiments, ZD is CH2NHCO and R9 is straight or branched C1-6 alkyl optionally substituted with halo, oxo, hydroxyl, or an optionally substituted group selected from aliphatic, cyclic, aryl, heteroaryl, alkoxy, amino, carboxyl, or carbonyl. In one embodiment, ZD is CH2NHCO and R9 is methyl. In one embodiment, ZD is CH2NHCO and R9 is CF3. In one embodiment, ZD is CH2NHCO and R9 is t-butoxy.
[00294] In one embodiment, ZD is SO2NH and R9 is H. In some embodiments, ZD is SO2NH and R9 is an optionally substituted straight or branched C1-6 aliphatic. In some embodiments, ZD is SO2NH and R9 is is straight or branched Ci-6 alkyl optionally substituted with halo, oxo, hydroxyl, or an optionally substituted group selected from C1-6 aliphatic, 3-8 membered cyclic, C6-1O aryl, 5-8 membered heteroaryl, alkoxy, amino, amido, carboxyl, or carbonyl. In one embodiment, ZD is SO2NH and R9 is methyl. In one embodiment, ZD is SO2NH and R9 is ethyl. In one embodiment, ZD is SO2NH and R9 is /-propyl. In one embodiment, ZD is SO2NH and R9 is t-butyl. In one embodiment, ZD is SO2NH and R9 is 3,3- dimethylbutyl. In one embodiment, ZD is SO2NH and R9 is CH2CH2OH. In one embodiment, ZD is SO2NH and R9 is CH(CH3)CH2OH. In one embodiment, ZD is SO2NH and R9 is CH2CH(CH3)OH. In one embodiment, ZD is SO2NH and R9 is CH(CH2OH)2. In one embodiment, ZD is SO2NH and R9 is CH2CH(OH)CH2OH. In one embodiment, ZD is SO2NH and R9 is CH2CH(OH)CH2CH3. In one embodiment, ZD is SO2NH and R9 is C(CH3)2CH2OH. In one embodiment, ZD is SO2NH and R9 is CH(CH2CH3)CH2OH. In one embodiment, ZD is SO2NH and R9 is CH2CH2OCH2CH2OH. In one embodiment, ZD is SO2NH and R9 is C(CH3)(CH2OH)2. In one embodiment, ZD is SO2NH and R9 is CH2CH(OH)CH2C(O)OH. In one embodiment, ZD is SO2NH and R9 is CH2CH2N(CH3)2. In one embodiment, ZD is SO2NH and R9 is CH2CH2NHC(O)CH3. In one embodiment, ZD is SO2NH and R9 is CH(CH(CH3)2)CH2OH. In one embodiment, ZD is SO2NH and R9 is CH(CH2CH2CH3)CH2OH. In one embodiment, ZD is SO2NH and R9 is 1-tetrahydrofuryl-methyl. In one embodiment, Z is SO2NH and R9 is furylmethyl. In one embodiment, ZD is SO2NH and R9 is (5-methylfuryl)- methyl. In one embodiment, ZD is SO2NH and R9 is 2-pyrrolidinylethyl. In one embodiment, ZD is SO2NH and R9 is 2-(l-methylpyrrolidinyl)-ethyl. In one embodiment, ZD is SO2NH and R9 is 2-(4-morpholinyl)-ethyl. In one embodiment, ZD is SO2NH and R9 is 3-(4-morpholinyl)- propyl. In one embodiment, ZD is SO2NH and R9 is C(CH2CH3)(CH2OH)2. In one embodiment, ZD is SO2NH and R9 is 2-(lH-imidazol~4-yl)ethyl. In one embodiment, ZD is SO2NH and R9 is 3-(lH-imidazol-l-yl)~propyl. In one embodiment, ZD is SO2NH and R9 is 2- (2-pyridinyl)-ethyl.
[00295] In some embodiment, ZD is SO2NH and R9 is an optionally substituted
CJ-6 cycloaliphatic. In several examples, ZD is SO2NH and R9 is an optionally substituted C1-6 cycloalkyl. In several examples, ZD is SO2NH and R9 is C1-6 cycloalkyl. In one embodiment, ZD is SO2NH and R9 is cyclobutyl. In one embodiment, ZD is SO2NH and R9 is cyclopentyl. In one embodiment, ZD is SO2NH and R9 is cyclohexyl.
[00296] In some embodiments, ZD is SO2N(C1-6 alkyl) and R9 is an optionally substituted straight or branched C1-6 aliphatic or an optionally substituted cycloaliphatic. In some embodiments, ZD is SO2N(C1-6 alkyl) and R9 is an optionally substituted straight or branched Ci-6 aliphatic. In some embodiments, ZD is SO2N(Ci-6 alkyl) and R9 is an optionally substituted straight or branched C1-6 alkyl or an optionally substituted straight or branched C1-6 alkenyl. In one embodiments, ZD is SO2N(CH3) and R9 is methyl. In one embodiments, ZD is SO2N(CH3) and R9 is n-propyl. In one embodiments, ZD is SO2N(CH3) and R9 is n-butyl. In one embodiments, ZD is SO2N(CH3) and R9 is cyclohexyl. In one embodiments, ZD is SO2N(CH3) and R9 is allyl. In one embodiments, ZD is SO2N(CH3) and R9 is CH2CH2OH. In one embodiments, ZD is SO2N(CH3) and R9 is CH2CH(OH)CH2OH. In one embodiments, ZD is SO2N(CH2CH2CH3) and R9 is cyclopropylmethyl.
[00297] In one embodiment, ZD is CH2NHSO2 and R9 is methyl. In one embodiment, ZD is CH2N(CH3)SO2 and R9 is methyl.
[00298] In some embodiments, ZD is SO2 and R9 is an optionally substituted C1-6 straight or branched aliphatic or an optionally substituted 3-8 membered heterocyclic, having 1, 2, or 3 ring members selected from the group consisting of nitrogen, oxygen, sulfur, SO, or SO2. In some embodiments, ZD is SO2 and R9 is straight or branched Ci-6 alkyl or 3-8 membered heterocycloaliphatic each of which is optionally substituted with 1, 2, or 3 of oxo, halo, hydroxyl, or an optionally substituted group selected from Ci-6 aliphatic, carbonyl, amino, and carboxy. In one embodiment, ZD is SO2 and R9 is methyl. In some embodiments, Z is SO2 and examples of R9 include
Figure imgf000058_0001
Figure imgf000059_0001
[00299] In some embodiments, RD2 is H, hydroxyl, halo, C1-6 alkyl, C1-6 alkoxy,
C3-6 cycloalkyl, or NH2. In several examples, RD2 is H, halo, C1-4 alkyl, or C1-4 alkoxy. Examples of RD2 include H, F, Cl, methyl, ethyl, and methoxy.
[00300] IN some embodiments, the present invention provides compounds of formula (I'-A) or formula (I'-B):
Figure imgf000059_0002
or a pharmaceutically acceptable salt thereof, wherein R1, R2, R3, R'3, R4, and n are defined above.
[00301] In some embodiments, R1 is an optionally substituted aryl. In several examples, R1 is phenyl optionally substituted with 1, 2, or 3 of halo, OH, -0( C1-6 aliphatic), amino, C1-6 aliphatic, C3-7 cycloaliphatic, 3-8 membered heterocycloaliphatic, C6-10 aryl, or 5-8 membered heteroaryl. In some embodiments, Ri is phenyl optionally substituted with alkoxy, halo, or amino. In one embodiment, R1 is phenyl. In one embodiment, R1 is phenyl substituted with Cl, methoxy, ethoxy, or dimethylamino.
[00302] In some embodiments, R2 is hydrogen. In some embodiments, R2 is optionally substituted C1-6 aliphatic.
[00303] In some embodiments, R3, R'3, and the carbon atom to which they are attached form an optionally substituted C3-8 cycloaliphatic or an optionally substituted 3-8 membered heterocycloaliphatic. In some embodiments, R3, R3, and the carbon atom to which they are attached form an optionally substituted C3-8 cycloalkyl. In one example, R3, R'3, and the carbon atom to which they are attached is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl or cycloheptyl, each of which is optionally substituted. In one example, R3, R'3, and the carbon atom to which they are attached is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl or cycloheptyl. In several examples, R3, R'3, and the carbon atom to which they are attached is cyclopropyl.
[00304] In some embodiments, R4 is an optionally substituted aryl or an optionally substituted heteroaryl. In some embodiments, R4 is an optionally substituted phenyl. In several embodiments, R4 is phenyl fused to a 3, 4, 5, or 6 membered heterocyclic having 1, 2, or 3 ring membered selected from oxygen, sulfur and nitrogen. In several embodiments, R4 is
X
, wherein T is defined above. In several examples, T is -CH2-.
[00305] Alternative embodiments of Rj, R2, R3, R3, R4, and n in formula (I*- A) or formula (I'-B) are as defined for formula (ϊ), formula (I1), and embodiments thereof.
[003061 Exemplary compounds of the present invention include, but are not limited to, those illustrated in Table 1 below. [00307] Table 1 : Examples of compounds of the present invention
Figure imgf000061_0001
Figure imgf000062_0001
Figure imgf000063_0001
Figure imgf000064_0001
Figure imgf000065_0001
Figure imgf000066_0001
Figure imgf000067_0001
Figure imgf000068_0001
Figure imgf000069_0001
Figure imgf000070_0001
Figure imgf000071_0001
Figure imgf000072_0001
Figure imgf000073_0001
Figure imgf000074_0001
Figure imgf000075_0001
Figure imgf000076_0001
Figure imgf000077_0001
Figure imgf000078_0001
Figure imgf000079_0001
Figure imgf000080_0001
Figure imgf000081_0001
Figure imgf000082_0001
Figure imgf000083_0001
Figure imgf000084_0001
Figure imgf000085_0001
Figure imgf000086_0001
Figure imgf000087_0001
Figure imgf000088_0001
Figure imgf000089_0001
Figure imgf000090_0001
Figure imgf000091_0001
Figure imgf000092_0001
Figure imgf000093_0001
Figure imgf000094_0001
Figure imgf000095_0001
Figure imgf000096_0001
Figure imgf000097_0001
SYNTHETIC SCHEMES
[00308] Compounds of the invention may be prepared by known methods or as illustrated in the examples. In one instance wherein R1 is aryl or heteroaryl, the compounds of the invention may be prepared as illustrated in Scheme I. [00309] Scheme I
Figure imgf000098_0001
a) 50% NaOH, X-R3-Rs-Y, BTEAC; X, Y= leaving group; b) SOCl2, DMF; c) pyridine; d) R1-B(OR)2, Pd(dpρf)Cl2, K2CO3, DMF, H2O
[00310] Scheme II
Figure imgf000098_0002
a) Pd(PPh3)4, CO, MeOH; b) LiAlH4, THF; c) SOCl2; d) NaCN; e) NBS or NCS, AIBN1 CX4 (X = Br Or Cl)
[00311] Scheme III
Figure imgf000099_0001
I a) pyridine, DCM; b) R1-B(OR)2, Pd(dppf)Cl2, K2CO3, DMF, H2O [00312] Scheme IV
Figure imgf000099_0002
a) pyridine, DCM; b) Ri-B(OR)2, Pd(dppf)Cl2, K2CO3, DMF, H2O
[00313] Referring to Scheme I, a nitrite of formula i is alkylated (step a) with a dihalo-aliphatic in the presence of abase such as, for example, 50% sodium hydroxide and, optionally, a phase transfer reagent such as, for example, benzyltriethylammonium chloride (BTEAC), to produce the corresponding alkylated nitrile (not shown) which on hydrolysis produces the acid ii. Compounds of formula ii are converted to the acid chloride iii with a suitable reagent such as, for example, thionyl chloride/DMF. Reaction of the acid chloride iii with an aminopyridine, wherein X is a halo, of formula iv (step c) produces the amide of formula v. Reaction of the amide v with an optionally substituted boronic acid derivative (step d) in the presence of a catalyst such as, for example, palladium acetate or dichloro-[l,l- bis(diρhenylphosphino) ferrocene] palladium(H) (Pd(dppf)Cl2 ) , provides compounds of the invention wherein R1 is aryl, heteroaryl, or cycloalkenyl. The boronic acid derivatives vi are commercially available or may be prepared by known methods such as reaction of an aryl bromide with a diborane ester in the presence of a coupling reagent such as, for example, palladium acetate as described in the examples.
[00314] In another instance where one R1 is aryl and another R1 is an aliphatic, alkoxy, cycloaliphatic, or heterocycloaliphatic, compounds of the invention can be prepared as described in steps a, b, and c of Scheme I using an appropriately substituted aminopyridine such
as
Figure imgf000100_0001
5 where X is halo and Q is C1-6 aliphatic, aryl, heteroaryl, or 3 to 10 membered cycloaliphatic or heterocycloaliphatic as a substitute for the aminopyridine of formula iv.
FORMULATIONS. ADMINISTRATIONS. AND USES Pharmaceutically acceptable compositions
[00315] Accordingly, in another aspect of the present invention, pharmaceutically acceptable compositions are provided, wherein these compositions comprise any of the compounds as described herein, and optionally comprise a pharmaceutically acceptable carrier, adjuvant or vehicle. In certain embodiments, these compositions optionally further comprise one or more additional therapeutic agents.
[00316] It will also be appreciated that certain of the compounds of present invention can exist in free form for treatment, or where appropriate, as a pharmaceutically acceptable derivative or a prodrug thereof. According to the present invention, a pharmaceutically acceptable derivative or a prodrug includes, but is not limited to, pharmaceutically acceptable salts, esters, salts of such esters, or any other adduct or derivative which upon administration to a patient in need is capable of providing, directly or indirectly, a compound as otherwise described herein, or a metabolite or residue thereof.
[00317] As used herein, the term "pharmaceutically acceptable salt" refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. A "pharmaceutically acceptable salt" means any non-toxic salt or salt of an ester of a compound of this invention that, upon administration to a recipient, is capable of providing, either directly or indirectly, a compound of this invention or an inhibitorily active metabolite or residue thereof.
[00318] Pharmaceutically acceptable salts are well known in the art. For example,
S. M. Berge, et al. describe pharmaceutically acceptable salts in detail in J. Phaπnaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference. Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p- toluenesulfonate, undecanoate, valerate salts, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(C1-4EIkVl)4 salts. This invention also envisions the quaternization of any basic nitrogen-containing groups of the compounds disclosed herein. Water or oil-soluble or dispersable products may be obtained by such quaternization. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate and aryl sulfonate.
[00319] As described above, the pharmaceutically acceptable compositions of the present invention additionally comprise a pharmaceutically acceptable carrier, adjuvant, or vehicle, which, as used herein, includes any and all solvents, diluents, or other liquid vehicle, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired. Remington: The Science and Practice of Pharmacy, 21st edition, 2005, ed. D.B. Troy, Lippincott Williams & Wilkins, Philadelphia, and Encyclopedia of Pharmaceutical Technology, eds. J. Swarbrick and J. C. Boylan, 1988-1999, Marcel Dekker, New York, the contents of each of which is incorporated by reference herein, disclose various carriers used in formulating pharmaceutically acceptable compositions and known techniques for the preparation thereof. Except insofar as any conventional carrier medium is incompatible with the compounds of the invention, such as by producing any undesirable biological effect or otherwise interacting in a deleterious manner with any other comρonent(s) of the pharmaceutically acceptable composition, its use is contemplated to be within the scope of this invention. Some examples of materials which can serve as pharmaceutically acceptable carriers include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, or potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, wool fat, sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil; safflower oil; sesame oil; olive oil; corn oil and soybean oil; glycols; such a propylene glycol or polyethylene glycol; esters such as ethyl oleate and ethyl laurate; agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non-toxic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the composition, according to the judgment of the formulator.
Uses of compounds and pharmaceutically acceptable compositions
[00320] In yet another aspect, the present invention provides a method of treating a condition, disease, or disorder implicated by ABC transporter activity. In certain embodiments, the present invention provides a method of treating a condition, disease, or disorder implicated by a deficiency of ABC transporter activity, the method comprising administering a composition comprising a compound of formulae (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B) to a subject, preferably a mammal, in need thereof.
[00321] In certain preferred embodiments, the present invention provides a method of treating Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronernia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay~Sachs, Crigler-Najjar type π, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1, Hereditary emphysema, Congenital hyperthyroidism, Osteogenesis imperfecta, Hereditary hypofibrinogenemia, ACT deficiency, Diabetes insipidus (DI), Neurophyseal DI, Neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders such as Huntington, Spinocerebullar ataxia type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt- Jakob disease (due to Prion protein processing defect), Fabry disease, Straussler-Scheinker disease, secretory diarrhea, polycystic kidney disease, chronic obstructive pulmonary disease (COPD), dry eye disease, and Sjogren's Syndrome, comprising the step of administering to said mammal an effective amount of a composition comprising a compound of formulae (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B), or a preferred embodiment thereof as set forth above.
[00322] According to an alternative preferred embodiment, the present invention provides a method of treating cystic fibrosis comprising the step of administering to said mammal a composition comprising the step of administering to said mammal an effective amount of a composition comprising a compound of formulae (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B), or a preferred embodiment thereof as set forth above.
[00323] According to the invention an "effective amount" of the compound or pharmaceutically acceptable composition is that amount effective for treating or lessening the severity of one or more of Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1, Hereditary emphysema, Congenital hyperthyroidism, Osteogenesis imperfecta, Hereditary hypofibrinogenemia, ACT deficiency, Diabetes insipidus (DI), Neurophyseal DI, Neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntmgton, Spinocerebullar ataxia type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt-Jakob disease, Fabry disease, Straussler-Scheinker disease, secretory diarrhea, polycystic kidney disease, chronic obstructive pulmonary disease (COPD), dry eye disease, and Sjogren's Syndrome.
[00324] The compounds and compositions, according to the method of the present invention, may be administered using any amount and any route of administration effective for treating or lessening the severity of one or more of Cystic fibrosis, Hereditary emphysema, Hereditary hemochromatosis, Coagulation-Fibrinolysis deficiencies, such as Protein C deficiency, Type 1 hereditary angioedema, Lipid processing deficiencies, such as Familial hypercholesterolemia, Type 1 chylomicronemia, Abetalipoproteinemia, Lysosomal storage diseases, such as I-cell disease/Pseudo-Hurler, Mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, Polyendocrinopathy/Hyperinsulemia, Diabetes mellitus, Laron dwarfism, Myleoperoxidase deficiency, Primary hypoparathyroidism, Melanoma, Glycanosis CDG type 1, Hereditary emphysema, Congenital hyperthyroidism, Osteogenesis imperfecta, Hereditary hypofibrinogenemia, ACT deficiency, Diabetes insipidus (DI), Neurophyseal DI, Neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, Progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, Spinocerebullar ataxia'type I, Spinal and bulbar muscular atrophy, Dentatorubal pallidoluysian, and Myotonic dystrophy, as well as Spongiform encephalopathies, such as Hereditary Creutzfeldt-Jakob disease, Fabry disease, Straussler-Scheinker disease, secretory diarrhea, polycystic kidney disease, chronic obstructive pulmonary disease (COPD), dry eye disease, and Sjogren's Syndrome.
[00325] The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular agent, its mode of administration, and the like. The compounds of the invention are preferably formulated in dosage unit form for ease of administration and uniformity of dosage. The expression "dosage unit form" as used herein refers to a physically discrete unit of agent appropriate for the patient to be treated. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific effective dose level for any particular patient or organism will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed, and like factors well known in the medical arts. The term "patient", as used herein, means an animal, preferably a mammal, and most preferably a human.
[00326] The pharmaceutically acceptable compositions of this invention can be administered to humans and other animals orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, or drops), bucally, as an oral or nasal spray, or the like, depending on the severity of the infection being treated. In certain embodiments, the compounds of the invention may be administered orally or parenterally at dosage levels of about 0.01 mg/kg to about 50 mg/kg and preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.
[00327] Liquid dosage forms for oral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active compounds, the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.
[00328] Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S. P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables. [00329] The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
[00330] In order to prolong the effect of a compound of the present invention, it is often desirable to slow the absorption of the compound from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the compound then depends upon its rate of dissolution that, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered compound form is accomplished by dissolving or suspending the compound in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the compound in biodegradable polymers such as polylactide-polyglycolide. Depending upon the ratio of compound to polymer and the nature of the particular polymer employed, the rate of compound release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the compound in liposomes or microemulsions that are compatible with body tissues.
[00331] Compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
[00332] Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar— agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may also comprise buffering agents.
[00333] Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polethylene glycols and the like.
[00334] The active compounds can also be in microencapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. 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, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes.
[00335] Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches. The active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required. Ophthalmic formulation, eardrops, and eye drops are also contemplated as being within the scope of this invention. Additionally, the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms are prepared by dissolving or dispensing the compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.
[00336] As described generally above, the compounds of the invention are useful as modulators of ABC transporters. Thus, without wishing to be bound by any particular theory, the compounds and compositions are particularly useful for treating or lessening the severity of a disease, condition, or disorder where hyperactivity or inactivity of ABC transporters is implicated in the disease, condition, or disorder. When hyperactivity or inactivity of an ABC transporter is implicated in a particular disease, condition, or disorder, the disease, condition, or disorder may also be referred to as an "ABC transporter-mediated disease, condition or disorder". Accordingly, in another aspect, the present invention provides a method for treating or lessening the severity of a disease, condition, or disorder where hyperactivity or inactivity of an ABC transporter is implicated in the disease state.
[00337] The activity of a compound utilized in this invention as a modulator of an
ABC transporter may be assayed according to methods described generally in the art and in the Examples herein.
[00338] It will also be appreciated that the compounds and pharmaceutically acceptable compositions of the present invention can be employed in combination therapies, that is, the compounds and pharmaceutically acceptable compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. The particular combination of therapies (therapeutics or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutics and/or procedures and the desired therapeutic effect to be achieved. It will also be appreciated that the therapies employed may achieve a desired effect for the same disorder (for example, an inventive compound may be administered concurrently with another agent used to treat the same disorder), or they may achieve different effects (e.g., control of any adverse effects). As used herein, additional therapeutic agents that are normally administered to treat or prevent a particular disease, or condition, are known as "appropriate for the disease, or condition, being treated".
[00339] The amount of additional therapeutic agent present in the compositions of this invention will be no more than the amount that would normally be administered in a composition comprising that therapeutic agent as the only active agent. Preferably the amount of additional therapeutic agent in the presently disclosed compositions will range from about 50% to 100% of the amount normally present in a composition comprising that agent as the only therapeutically active agent.
[00340] The compounds of this invention or pharmaceutically acceptable compositions thereof may also be incorporated into compositions for coating an implantable medical device, such as prostheses, artificial valves, vascular grafts, stents and catheters. Accordingly, the present invention, in another aspect, includes a composition for coating an implantable device comprising a compound of the present invention as described generally above, and in classes and subclasses herein, and a carrier suitable for coating said implantable device. In still another aspect, the present invention includes an implantable device coated with a composition comprising a compound of the present invention as described generally above, and in classes and subclasses herein, and a carrier suitable for coating said implantable device. Suitable coatings and the general preparation of coated implantable devices are described in US Patents 6,099,562; 5,886,026; and 5,304,121. The coatings are typically biocompatible polymeric materials such as a hydrogel polymer, polymethyldisiloxane, polycaprolactone, polyethylene glycol, polylactic acid, ethylene vinyl acetate, and mixtures thereof. The coatings may optionally be further covered by a suitable topcoat of fluorosilicone, polysaccarides, polyethylene glycol, phospholipids or combinations thereof to impart controlled release characteristics in the composition.
[00341] Another aspect of the invention relates to modulating ABC transporter activity in a biological sample or a patient (e.g., in vitro or in vivo), which method comprises administering to the patient, or contacting said biological sample with a compound of formula I or a composition comprising said compound. The term "biological sample", as used herein, includes, without limitation, cell cultures or extracts thereof; biopsied material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts thereof.
[00342] Modulation of ABC transporter activity in a biological sample is useful for a variety of purposes that are known to one of skill in the art. Examples of such purposes include, but are not limited to, the study of ABC transporters in biological and pathological phenomena; and the comparative evaluation of new modulators of ABC transporters.
[00343] In yet another embodiment, a method of modulating activity of an anion channel in vitro or in vivo, is provided comprising the step of contacting said channel with a compound of formulae (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B). In preferred embodiments, the anion channel is a chloride channel or a bicarbonate channel. In other preferred embodiments, the anion channel is a chloride channel. I>C T./llSQB /M-35e'g
[00344] According to an alternative embodiment, the present invention provides a method of increasing the number of functional ABC transporters in a membrane of a cell, comprising the step of contacting said cell with a compound of formula (I, II, III, IV, V-A, V- B, I', I'-A, and I'-B). The term "functional ABC transporter" as used herein means an ABC transporter that is capable of transport activity. In preferred embodiments, said functional ABC transporter is CFTR.
[00345] According to another preferred embodiment, the activity of the ABC transporter is measured by measuring the transmembrane voltage potential. Means for measuring the voltage potential across a membrane in the biological sample may employ any of the known methods in the art, such as optical membrane potential assay or other electrophysiological methods.
[00346] The optical membrane potential assay utilizes voltage-sensitive FRET sensors described by Gonzalez and Tsien (See, Gonzalez, J. E. and R. Y. Tsien (1995) "Voltage sensing by fluorescence resonance energy transfer in single cells" Biophys J 69(4): 1272-80, and Gonzalez, J. E. and R. Y. Tsien (1997) "Improved indicators of cell membrane potential that use fluorescence resonance energy transfer" Chem Biol 4(4): 269-77) in combination with instrumentation for measuring fluorescence changes such as the Voltage/Ion Probe Reader (VIPR) (See, Gonzalez, J. E., K. Oades, et al. (1999) "Cell-based assays and instrumentation for screening ion-channel targets" Drug Discov Today 4(9): 431-439).
[00347] These voltage sensitive assays are based on the change in fluorescence resonant energy transfer (FRET) between the membrane-soluble, voltage-sensitive dye, DiSBAC2(3), and a fluorescent phospholipid, CC2-DMPE, which is attached to the outer leaflet of the plasma membrane and acts as a FRET donor. Changes in membrane potential (Vm) cause the negatively charged DiSBAC2(3) to redistribute across the plasma membrane and the amount of energy transfer from CC2-DMPE changes accordingly. The changes in fluorescence emission can be monitored using VEPR™ II, which is an integrated liquid handler and fluorescent detector designed to conduct cell-based screens in 96- or 384-well microtiter plates.
[00348] In another aspect the present invention provides a kit for use in measuring the activity of a ABC transporter or a fragment thereof in a biological sample in vitro or in vivo comprising (i) a composition comprising a compound of formula (I, II, III, IV, V-A, V-B, I', I'-A, and I'-B) or any of the above embodiments; and (ii) instructions for a.) contacting the composition with the biological sample and b.) measuring activity of said ABC transporter or a fragment thereof. In one embodiment, the kit further comprises instructions for a.) contacting an additional composition with the biological sample; b.) measuring the activity qf said ABC transporter or a fragment thereof in the presence of said additional compound, and c.) comparing the activity of the ABC transporter in the presence of the additional compound with the density of the ABC transporter in the presence of a composition of formula (I, II, III, IV, V- A, V-B, I', I'-A, and V-B). In preferred embodiments, the 3dt is used to measure the density of CFTR.
PREPARATIONS AND EXAMPLES General Procedwe I; Carboxylic Acid Building Block
Figure imgf000111_0001
Hal = Cl, Br, I
[00349] Benzyltriethylammonium chloride (0.025 equivalents) and the appropriate dihalo compound (2.5 equivalents) were added to a substituted phenyl acetonitrile. The mixture was heated at 700C and then 50% sodium hydroxide (10 equivalents) was slowly added to the mixture. The reaction was stirred at 700C for 12-24 hours to ensure complete formation of the cycloalkyl moiety and then heated at 1300C for 24-48 hours to ensure complete conversion from the nitrile to the carboxylic acid. The dark brown / black reaction mixture was diluted with water and extracted with ethyl acetate and then dichloromethane three times each to remove side products. The basic aqueous solution was acidified with concentrated hydrochloric acid to pH less than one and the precipitate which began to form at pH 4 was filtered and washed with 1 M hydrochloric acid two times. The solid material was dissolved in dichloromethane and extracted two times with 1 M hydrochloric acid and one time with a saturated aqueous solution of sodium chloride. The organic solution was dried over sodium sulfate and evaporated to dryness to give the cycloalkylcarboxylic acid.
A. l-Benzofl,31dioxol-5-yl-cyclopropanecarboxylic acid
Figure imgf000111_0002
[00350] A mixture of benzo[l,3]dioxole-5-acetonitrile (5.10 g, 31.7 mmol), 1- bromo-2'Chloro-ethane (9.00 mL, 109 mmol), and benzyltriethylammonium chloride (0.181 g, 0.795 mmol) was heated at 70 0C and then 50% (wt./wt.) aqueous sodium, hydroxide (26 mL) was slowly added to the mixture. The reaction was stirred at 70 0C for 18 hours and then heated
- UO - at 130 0C for 24 hours. The dark brown reaction mixture was diluted with water (400 mL) and extracted once with an equal volume of ethyl acetate and once with an equal volume of dichloromethane. The basic aqueous solution was acidified with concentrated hydrochloric acid to pH less than one and the precipitate filtered and washed with 1 M hydrochloric acid. The solid material was dissolved in dichloromethane (400 mL) and extracted twice with equal volumes of 1 M hydrochloric acid and once with a saturated aqueous solution of sodium chloride. The organic solution was dried over sodium sulfate and evaporated to dryness to give a white to slightly off-white solid (5.23 g, 80%) ESI-MS m/z calc. 206.1, found 207.1 (M+l)+. Retention time of 2.37 minutes. 1H NMR (400 MHz, DMSCM6) δ 1.07-1.11 (m, 2H), 1.38-1.42 (m, 2H), 5.98 (s, 2H), 6.79 (m, 2H), 6.88 (m, IH), 12.26 (s, IH).
General Procedure H: Carboxyiic Acid Building Block
Figure imgf000112_0001
Hal = Cl, Br, I1 all other variables are as defined in the text.
[00351] Sodium hydroxide (50% aqueous solution, 7.4 equivalents) was slowly added to a mixture of the appropriate phenyl acetonitrile, benzyltriemylarnmonium chloride (1.1 equivalents), and the appropriate dihalo compound (2.3 equivalents) at 700C. The mixture was stirred overnight at 70 0C and the reaction mixture was diluted with water (30 mL) and extracted with ethyl acetate. The combined organic layers were dried over sodium sulfate and evaporated to dryness to give the crude cyclopropanecarbonitrile, which was used directly in the next step.
[00352] The crude cyclopropanecarbonitrile was heated at reflux in 10% aqueous sodium hydroxide (7.4 equivalents) for 2.5 hours. The cooled reaction mixture was washed with ether (100 mL) and the aqueous phase was acidified to pH 2 with 2M hydrochloric acid. The precipitated solid was filtered to give the cyclopropanecarboxylic acid as a white solid.
- Ill - IP" C T./'" U S Cl B /' 1!4'";;1 SB Φ
General Procedure Hl: Carboxyϋc Acid Building Block
Figure imgf000113_0001
Figure imgf000113_0002
B. 1 -(2,2-Difluoro-benzor 1 ,3]dioxol-5-yl)-cvclopropanecarboxylic acid
LiAIH4
Figure imgf000113_0004
Figure imgf000113_0003
Figure imgf000113_0005
[00353] Step a: 2,2-Difluoro-benzo[l,3]dioxole-5~carboxylic acid methyl ester
A solution of 5-bromo-2,2-difluoro-benzo[l,3]dioxole (11.8 g, 50.0 mrtiol) and tetrakis(triphenylphosphine)palladium (O) [Pd(PPh3)4, 5.78 g, 5.00 mmol] in methanol (20 mL) containing acetonitrile (30 mL) and triethylamine (10 mL) was stirred under a carbon monoxide atmosphere (55 PSI) at 75 0C (oil bath temperature) for 15 hours. The cooled reaction mixture was filtered and the filtrate was evaporated to dryness. The residue was purified by silica gel column chromatography to give crude 2,2-difluoro-benzo [1,3] dioxole-5- carboxylic acid methyl ester (11.5 g), which was used directly in the next step.
[00354] Step b: (2,2-Difluoro-benzo[l,3]dioxol-5-yl)-methanol
Crude 2,2-difluoro-benzo[l,3]dioxole-5-carboxyIic acid methyl ester (11.5 g) dissolved in 20 mL of anhydrous tetrahydrofuran (THF) was slowly added to a suspension of lithium aluminum hydride (4.10 g, 106 mmol) in anhydrous THF (100 mL) at 0 0C. The mixture was then warmed to room temperature. After being stirred at room temperature for 1 hour, the reaction mixture was cooled to 00C and treated with water (4.1 g), followed by sodium hydroxide (10% aqueous solution, 4.1 mL). The resulting slurry was filtered and washed with THF. The combined filtrate was evaporated to dryness and the residue was purified by silica gel column chromatography to give (2,2-difluoro-benzo[l,3]dioxol-5-yl)- methanol (7.2 g, 38 mmol, 76 % over two steps) as a colorless oil.
[00355] ■ Step c: 5-Chloromethyl-2,2-difluoro-benzo[l,3]dioxole
Thionyl chloride (45 g, 38 mmol) was slowly added to a solution of (2,2-difluoro- benzo[l,3]dioxol-5-yl)-methanol (7.2 g, 38 mmol) in dichloromethane (200 mL) at 0 0C. The resulting mixture was stirred overnight at room temperature and then evaporated to dryness. The residue was partitioned between an aqueous solution of saturated sodium bicarbonate (100 mL) and dichloromethane (100 mL). The separated aqueous layer was extracted with dichloromethane (150 mL) and the organic layer was dried over sodium sulfate, filtered, and evaporated to dryness to give crude 5-chloromethyl-2,2-difluoro-benzo[l,3]dioxole (4.4 g) which was used directly in the next step.
[00356] Step d: (2,2-Difluoro-benzo[l,3]dioxol-5-yl)-acetonitrile
A mixture of crude 5-chloromethyl-2,2-difluoro-benzo[l,3]dioxole (4.4 g) and sodium cyanide (1.36 g, 27.8 mmol) in dimethylsulfoxide (50 mL) was stirred at room temperature overnight. The reaction mixture was poured into ice and extracted with ethyl acetate (300 mL). The organic layer was dried over sodium sulfate and evaporated to dryness to give crude (2,2-difluoro-benzo[l,3]dioxol-5-yl)-acetonitrile (3.3 g) which was used directly in the next step.
[00357] Step e: l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarbonitrile
Sodium hydroxide (50% aqueous solution, 10 mL) was slowly added to a mixture of crude (2,2-difluoro-benzo[l,3]dioxol-5-yl)-acetonitrile, benzyltriethylammonium chloride (3.00 g, 15.3 mmol), and l-bromo-2-chloroethane (4.9 g, 38 mmol) at 70 0C. The mixture was stirred overnight at 700C before the reaction mixture was diluted with water (30 mL) and extracted with ethyl acetate. The combined organic layers were dried over sodium sulfate and evaporated to dryness to give crude l-(2,2-difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarbonitrile, which was used directly in the next step.
[00358] Step f: l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarboxylic acid l-(2,2-Difluoro-benzo[l,3]dioxol-5-yl)-cyclopropanecarbonitrile (crude from the last step) was refluxed in 10% aqueous sodium hydroxide (50 mL) for 2.5 hours. The cooled reaction mixture was washed with ether (100 mL) and the aqueous phase was acidified to pH 2 with 2M hydrochloric acid. The precipitated solid was filtered to give l-(2,2-difluoro- benzo[l,3]dioxol-5-yl)-cyclopropanecarboxylic acid as a white solid (0.15 g, 1.6% over four steps). ESI-MS m/z calc. 242.2, found 243.3 (M+l)+; 1H NMR (CDCl3) δ 7.14-7.04 (m, 2H), 6.98-6.96 (m, IH), 1.74-1.64 (m, 2H), 1.26-1.08 (m, 2H).
C. 2-(4-Chloro-3-methoxyphenyl)acetomtrile
Figure imgf000115_0001
Step a: l-Chloro-2-methoxy-4-methyl-benzene
To a solution of 2-chloro-5-methyl-phenol (93 g, 0.65 mol) in CH3CN (700 mL) was added CH3I (111 g, 0.78 mol) and K2CO3 (180 g, 1.3 mol). The mixture was stirred at 25 °C overnight. The solid was filtered off and the filtrate was evaporated under vacuum to give 1- chloro-2-methoxy-4-methyl-benzene (90 g, 89%). 1H NMR (300 MHz, CDCl3) δ 7.22 (d, J = 7.8 Hz, 1 H), 6.74-6.69 (m, 2 H), 3.88 (s, 3 H), 2.33 (s, 3 H).
[00360] Step b: 4-Bromomethyl-l-chloro-2-methoxy-benzene
To a solution of l-chloro-2-methoxy-4-methyl-benzene (50 g, 0.32 mol) in CCl4 (350 mL) was added NBS (57.2 g, 0.32 mol) and AIBN (10 g, 60 rnmol). The mixture was heated at reflux for 3 hours. The solvent was evaporated under vacuum and the residue was purified by column chromatography on silica gel (Petroleum Ether/EtOAc = 20:1) to give 4- bromomethyl-l-chloro-2-methoxy-benzene (69 g, 92%). 1H NMR (400 MHz, CDCl3) δ 7.33- 7.31 (m, 1 H), 6.95-6.91 (m, 2 H), 4.46 (s, 2 H), 3.92 (s, 3 H).
[00361] Step c: 2-(4-Chloro-3-methoxyphenyl)acetonitrile
To a solution of 4-bromomethyl-l-chloro-2-methoxy-benzene (68.5 g, 0.29 mol) in C2H5OH (90%, 500 mL) was added NaCN (28.5 g, 0.58 mol). The mixture was stirred at 60 0C overnight. Ethanol was evaporated and the residue was dissolved in H2O. The mixture was extracted with ethyl acetate (300 mL x 3). The combined organic layers were washed with brine, dried over Na2SO4 and purified by column chromatography on silica gel (Petroleum Ether/EtOAc 30:1) to give 2-(4-chloro-3-methoxyphenyl)acetonitrile (25 g, 48%). 1H NMR (400 MHz, CDCl3) δ 7.36 (d, J= 8 Hz, 1 H), 6.88-6.84 (m, 2 H), 3.92 (s, 3 H), 3.74 (s, 2 H). 13C NMR (100 MHz, CDCl3) δ 155.4, 130.8, 129.7, 122.4, 120.7, 117.5, 111.5, 56.2, 23.5. D. (4-Chloro-3-hydroxy- phenyl)-acetonitrile
Figure imgf000116_0001
[00362] BBr3 (16.6 g, 66 mmol) was slowly added to a solution of 2-(4-chloro-3- methoxyphenyl)acetonitrile (12 g, 66 mmol) in DCM (120 mL) at -78 0C under N2. The reaction temperature was slowly increased to room temperature. The reaction mixture was stirred overnight and then poured into ice-water. The organic layer was separated and the aqueous layer was extracted with DCM (40 mL x 3). The combined organic layers were washed with water, brine, dried over Na2SO4, and concentrated under vacuum to give (4-chloro- 3-hydroxy-phenyl)-acetonitrile (9.3 g, 85%). 1H NMR (300 MHz, CDCl3) δ 7.34 (d, J = 8.4 Hz, 1 H), 7.02 (d, J = 2.1 Hz, 1 H)7 6.87 (dd, /= 2.1, 8.4 Hz, 1 H), 5.15 (brs, IH), 3.72 (s, 2 H).
E. l-(3-(Ηvdroxymethyl)-4-methoxyr>henyl)cyclopropanecarboxylic acid
Na2CO3
Figure imgf000116_0002
Figure imgf000116_0003
[00363] Step a: l-(4-Methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester
To a solution of l-(4-methoxy-phenyl)-cyclopropanecarboxylic acid (50.0 g, 0.26 mol) in MeOH (500 mL) was added toluene-4-sulfonic acid monohydrate (2.5 g, 13 mmol) at room temperature. The reaction mixture was heated at reflux for 20 hours. MeOH was removed by evaporation under vacuum and EtOAc (200 mL) was added. The organic layer was washed with sat. aq. NaHCOs (100 mL) and brine, dried over anhydrous NaJSO4 and evaporated under vacuum to give l-(4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (53.5 g, 99%). 1H NMR (CDCl3, 400 MHz) δ 7.25-7.27 (m, 2 H), 6.85 (d, /= 8.8 Hz, 2 H), 3.80 (s, 3 H), 3.62 (s, 3 H), 1.58 (m, 2 H), 1.15 (m, 2 H).
[00364] Step b: l-(3-Chloromethyl~4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester
To a solution of l-(4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (30.0 g, 146 mmol) and MOMCl (29.1 g, 364 mmol) in CS2 (300 mL) was added TiCl4 (8.30 g, 43.5 mmol) at 5 0C. The reaction mixture was heated at 30 0C for 1 day and poured into ice- water. The mixture was extracted with CH2Cl2 (150 mL x 3). The combined organic extracts P CT w/eUreS evOapBora/ted«* u3nydδerS va«c3uum to gi .ve crud Je l Λ- ,(3.-ch . .loromet ,hyl ,-4 „-met uhoxy-ph ueny 1lN)- cyclopropanecarboxylic acid methyl ester (38.0 g), which was used in the next step without further purification.
[00365] Step c: l-(3-Hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester
To a suspension of crude l-(3-chloromethyl-4-methoxy-phenyl)- cyclopropanecarboxylic acid methyl ester (20.0 g) in water (350 mL) was added Bu4NBr (4.0 g) and Na2CO3 (90.0 g, 0.85 mol) at room temperature. The reaction mixture was heated at 65 0C overnight. The resulting solution was acidified with aq. HCl (2 mol/L) and extracted with EtOAc (200 mL x 3). The organic layer was washed with brine, dried over anhydrous Na2SO4 and evaporated under vacuum to give crude product, which was purified by column (Petroleum Ether/EtOAc 15:1) to give l-(3-hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (8.0 g, 39%). 1H NMR (CDCl3, 400 MHz) δ 7.23-7.26 (m, 2 H), 6.83 (d, J = 8.0 Hz, 1 H), 4.67 (s, 2 H), 3.86 (s, 3 H), 3.62 (s, 3 H), 1.58 (q, /= 3.6 Hz, 2 H), 1.14-1.17 (m, 2 H).
[00366] Step d: l-[3-(ϊert-Butyl-dimethyl-silanyloxymethyl)-4-methoxy- phenyl]cyclopropane-carboxylic acid methyl ester
To a solution of l-(3-hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid methyl ester (8.0 g, 34 mmol) in CH2Cl2 (100 mL) were added imidazole (5.8 g, 85 mmol) and TBSCl (7.6 g, 51 mmol) at room temperature. The mixture was stirred overnight at room temperature. The mixture was washed with brine, dried over anhydrous Na2SO4 and evaporated under vacuum to give crude product, which was purified by column (Petroleum Ether/EtOAc 30:1) to give l-[3-(te/t-butyl-dimethyl-silanyloxymethyl)-4-methoxy-phenyl]- cyclopropanecarboxylic acid methyl ester (6.7 g, 56%). 1H NMR (CDCl3, 400 MHz) δ 7.44- 7.45 (m, 1 H), 7.19 (dd, J = 2.0, 8.4 Hz, 1 H), 6.76 (d, /= 8.4 Hz, 1 H), 4.75 (s, 2 H), 3.81 (s, 3 H), 3.62 (s, 3 H), 1.57-1.60 (m, 2 H), 1.15- 1.18 (m, 2 H), 0.96 (s, 9 H), 0.11 (s, 6 H).
[00367] Step e: l-(3-Hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid
To a solution of l-[3-(^r?-butyl-dimethyl-silanyloxymethyl)-4-methoxy-phenyl]- cyclopropanecarboxylic acid methyl ester (6.2 g, 18 mmol) in MeOH (75 mL) was added a solution of LiOH.H2O (1.50 g, 35.7 mmol) in water (10 mL) at 0 0C. The reaction mixture was stirred overnight at 40 0C. MeOH was removed by evaporation under vacuum. AcOH (1 mol/L, 40 mL) and EtOAc (200 mL) were added. The organic layer was separated, washed x
Figure imgf000118_0001
Nτa2S crOk4 and , evapora tted A und Aer vacuum to provi .d,e l .- „(3- hydroxymethyl-4-methoxy-phenyl)-cyclopropanecarboxylic acid (5.3 g).
F. 2-(3-Fluoro-4-methoxyphenyl)acetonitrile
Figure imgf000118_0002
[00368] To a suspension of t-BuOK (25.3 g, 0.207 mol) in THF (150 mL) was added a solution of TosMIC (20.3 g, 0.104 mol) in THF (50 mL) at -78 °C. The mixture was stirred for 15 minutes, treated with a solution of 3-fluoro-4-methoxy-benzaldehyde (8.00 g, 51.9 mmol ) in THF (50 mL) dropwise, and continued to stir for 1.5 hours at -78 0C. To the cooled reaction mixture was added methanol (50 mL). The mixture was heated at reflux for 30 minutes. Solvent of the reaction mixture was removed to give a crude product, which was dissolved in water (200 mL). The aqueous phase was extracted with EtOAc (100 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give crude product, which was purified by column chromatography (Petroleum Ether/EtOAc 10:1) to afford 2-(3-fluoro-4-methoxyphenyl)acetonitrile (5.0 g, 58%). 1H NMR (400 MHz, CDCl3) δ 7.02-7.05 (m, 2 H), 6.94 (t, J= 8.4 Hz, 1 H), 3.88 (s, 3 H), 3.67 (s, 2 H). 13C NMR (100 MHz, CDCl3) δ 152.3, 147.5, 123.7, 122.5, 117.7, 115.8, 113.8, 56.3, 22.6.
G. 2-(3-Chloro-4-methoxyphenyl)acetonitrile
Figure imgf000118_0003
[00369] To a suspension of t-BuOK (4.8 g, 40 mmol) in THF (30 mL) was added a solution of TosMIC (3.9 g, 20 mmol) in THF (10 mL) at -78 0C. The mixture was stirred for 10 minutes, treated with a solution of 3-chloro-4-methoxy-benzaldehyde (1.65 g, 10 mmol ) in THF (10 mL) dropwise, and continued to stir for 1.5 hours at -78 0C. To the cooled reaction mixture was added methanol (10 mL). The mixture was heated at reflux for 30 minutes. Solvent of the reaction mixture was removed to give a crude product, which was dissolved in water (20 mL). The aqueous phase was extracted with EtOAc (20 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give crude product, which was purified by column chromatography (Petroleum Ether/EtOAc 10:1) to afford 2-(3-chloro-4- methoxyphenyl)acetonitrile (1.5 g, 83%). 1H NMR (400 MHz, CDCl3) δ 7.33 (d, J = 2.4 Hz, 1 H), 7.20 (dd, J = 2.4, 8.4 Hz, 1 H), 6.92 (d, J = 8.4 Hz, 1 H), 3.91 (s, 3 H), 3.68 (s, 2 H). 13C fp c ry y s o s ./ H-B 2 e 9
NMR (100 MHz, CDCl3) S 154.8, 129.8, 127.3, 123.0, 122.7, 117.60, 112.4, 56.2, 22.4. H. l-(3,3-Dim.ethyl-2,3-dihydrobenzofuran-5-γl)cyclopropanecarboxylic acid
Figure imgf000119_0001
[00370] Step a: l-(4-Hydroxy-ρhenyl)-cyclopropanecarboxylic acid methyl ester
To a solution of methyl l-(4-methoxyphenyl)cycloρropanecarboxylate (10.0 g, 48.5 mmol) in DCM (80 mL) was added EtSH (16 mL) under ice-water bath. The mixture was stirred at 0 0C for 20 min before AlCl3 (19.5 g, 0.15 mmol) was added slowly at 0 °C. The mixture was stirred at 0 0C for 30 min. The reaction mixture was poured into ice-water, the organic layer was separated, and the aqueous phase was extracted with DCM (50 mL x 3). The combined organic layers were washed with H2O, brine, dried over Na2SO4 and evaporated under vacuum to give l-(4-hydroxy-phenyl)-cycloproρanecarboxylic acid methyl ester (8.9 g, 95%). 1H NMR (400 MHz, CDCl3) δ 7.20-7.17 (m, 2 H), 6.75-6.72 (m, 2 H), 5.56 (s, 1 H), 3.63 (s, 3 H), 1.60-1.57 (m, 2 H), 1.17-1.15 (m, 2 H).
[00371] Step b: l-(4-Hydroxy-3,5-diiodo-phenyl)-cycloproρanecarboxylic acid methyl ester
To a solution of l-(4-hydroxy-phenyl)-cycloρropanecarboxylic acid methyl ester (8.9 g, 46 mmol) in CH3CN (80 mL) was added NIS (15.6 g, 69 mmol). The mixture was stirred at room temperature for 1 hour. The reaction mixture was concentrated and the residue was purified by column chromatography on silica gel (Petroleum Ether/EtOAc 10:1) to give 1- (4-hydroxy-3,5-diiodo~phenyl)-cycloρropanecarboxylic acid methyl ester (3.5 g, 18%). 1H NMR (400 MHz, CDCl3) δ 7.65 (s, 2 H), 5.71 (s, 1 H), 3.63 (s, 3 H), 1.59-1.56 (m, 2 H), 1.15- 1.12 (m, 2 H).
[00372] Step c: l-[3,5-Diiodo-4-(2-memyl-allyloxy)-phenyl]- cyclopropanecarboxylic acid methyl ester
A mixture of l-(4~hydroxy-3,5-diiodo~ρhenyl)-cyclopropanecarboxylic acid methyl ester (3.2 g, 7.2 mmol), 3-chloro-2-methyl-proρene (1.0 g, li mmol), K2CO3 (1.2 g, 8.6 mmol), NaI (0.1 g, 0.7 mmol) in acetone (20 mL) was stirred at 20 °C overnight. The solid was filtered off and the filtrate was concentrated under vacuum to give l-[3,5~diiodo-4~(2-methyl-allyloxy)- phenyl]-cycloρropane-carboxylic acid methyl ester (3.5 g, 97%). 1H NMR (300 MHz, CDCl3) δ 7.75 (s, 2 H), 5.26 (s, 1 H)5 5.06 (s, 1 H), 4.38 (s, 2 H), 3.65 (s, 3 H), 1.98 (s, 3H), 1.62-1.58 (m, 2 H), 1.18-1.15 (m, 2 H).
[00373] Step d: l-(3,3-Dimethyl-2,3-dihydro-benzofuran-5-yl)- cyclopropanecarboxylic acid methyl ester
To a solution of l-[3,5-diiodo-4-(2-methyl-allyloxy)-phenyl]-cycloproρane- carboxylic acid methyl ester (3.5 g, 7.0 mmol) in toluene (15 niL) was added Bu3SnH (2.4 g, 8.4 mmol) and AIBN (0.1 g, 0.7 mmol). The mixture was heated at reflux overnight. The reaction mixture was concentrated under vacuum and the residue was purified by column chromatography on silica gel (Petroleum Ether/EtO Ac 20:1) to give l-(3,3-dimethyl-2,3- dihydro-benzofuran-5-yl)-cycloρropanecarboxylic acid methyl ester (1.05 g, 62%). H NMR (400 MHz, CDCl3) δ 7.10-7.07 (m, 2 H), 6.71 (d, /= 8 Hz, 1 H), 4.23 (s, 2 H), 3.62 (s, 3 H), 1.58-1.54 (m, 2 H), 1.34 (s, 6 H), 1.17-1.12 (m, 2 H).
[00374] Step e: l-(3,3-Dimethyl-2,3-dihydrobenzofuran-5- yl)cycloρropanecarboxylic acid
To a solution of l-(3,3-dimethyl-2,3-dihydro-benzofuran-5-yl)- cyclopropanecarboxylic acid methyl ester (1 g, 4 mmol) in MeOH (10 mL) was added LiOH (0.40 g, 9.5 mmol). The mixture was stirred at 40 0C overnight. HCl (10%) was added slowly to adjust the pH to 5. The resulting mixture was extracted with ethyl acetate (10 mL x 3). The extracts were washed with brine and dried over Na2SO4. The solvent was removed under vaccum and the crude product was purified by preparative HPLC to give l-(3,3-dimethyl-2,3- dihydrobenzofuran-5-yl)cyclopropanecarboxylic acid (0.37 g, 41%). 1H NMR (400 MHz, CDCl3) δ 7.11-7.07 (m, 2 H), 6.71 (d, J = 8 Hz, 1 H), 4.23 (s, 2 H), 1.66-1.63 (m, 2 H), 1.32 (s, 6 H), 1.26-1.23 (m, 2 H).
I. 2-(7-Methoxybenzof di \ 1 ,31dioxol-5-yl)acetonitrile
Figure imgf000120_0001
P C T./ IJ S O B ,/' **.35 R B
[00375] Step a: 3,4-Dihydroxy-5-methoxybenzoate
To a solution of 3,4,5-trihydroxy-benzoic acid methyl ester (50 g, 0.27 mol) and Na2B4O7 (50 g) in water (1000 mL) was added Me2SO4(OO mL) and aqueous NaOH solution (25%, 200 mL) successively at room temperature. The mixture was stirred at room temperature for 6 h before it was cooled to 0 0C. The mixture was acidified to pH ~ 2 by adding cone. H2SO4 and then filtered. The filtrate was extracted with EtOAc (500 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated under reduced pressure to give methyl 3,4-dihydroxy-5-methoxybenzoate (15.3 g 47%), which was used in the next step without further purification.
[00376] Step b: Methyl 7-methoxybenzo[d] [ 1 ,3]dioxole-5-carboxylate
To a solution of methyl 3,4-dihydroxy-5-methoxybenzoate (15.3 g, 0.078 mol) in acetone (500 mL) was added CH2BrCl (34.4 g, 0.27 mol) and K2CO3 (75 g, 0.54 mol) at 80 0C. The resulting mixture was heated at reflux for 4 h. The mixture was cooled to room temperature and solid K2CO3 was filtered off. The filtrate was concentrated under reduced pressure, and the residue was dissolved in EtOAc (100 mL). The organic layer was washed with water, dried over anhydrous Na2SO4, and evaporated under reduced pressure to give the crude product, which was purified by column chromatography on silica gel (Petroleum Ether/Ethyl Acetate = 10:1) to afford methyl 7-methoxybenzo[d][l,3]dioxole-5-carboxylate (12.6 g, 80%). 1H NMR (400 MHz, CDCl3) δ 7.32 (s, 1 H), 7.21 (s, 1 H), 6.05 (s, 2 H), 3.93 (s, 3 H), 3.88 (s, 3 H).
[00377] Step c: (7-Methoxybenzo[d][l,3]dioxol-5-yl)methanol
To a solution of methyl 7-methoxybenzo[d][l,3]dioxole-5-carboxylate (13.9 g, 0.040 mόl) in THF (100 mL) was added LiAlH4 (3.1 g, 0.080 mol) in portions at room temperature. The mixture was stirred for 3 h at room temperature. The reaction mixture was cooled to 0 °C and treated with water (3.1 g) and NaOH (10%, 3.1 mL) successively. The slurry was filtered off and washed with THF. The combined filtrates were evaporated under reduced pressure to give (7-methoxy-benzo[d][l,3]dioxol-5-yl)methanol (7.2 g, 52%). 1H NMR (400 MHz, CDCl3) δ 6.55 (s, IH), 6.54 (s, IH), 5.96 (s, 2 H), 4.57 (s, 2 H), 3.90 (s, 3 H).
[00378] Step d: 6-(Chloromethyl)-4-methoxybenzo[d][l,3]dioxole
To a solution of SOCl2 (150 mL) was added (7~methoxybenzo[d][l,3]dioxol-5- yl)methanol (9.0 g, 54 mmol) in portions at 0 0C. The mixture was stirred for 0.5 h. The excess SOCl2 was evaporated under reduced pressure to give the crude product, which was basified with sat. aq. NaHCO3 to pH ~ 7. The aqueous phase was extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated to give 6- (chloromethyl)-4-methoxybenzo[d][l,3]dioxole (10.2 g 94%), which was used in the next step without further purification. 1H NMR (400 MHz, CDCl3) δ 6.58 (s, 1 H), 6.57 (s, 1 H), 5.98 (s, 2 H), 4.51 (s, 2 H), 3.90 (s, 3 H).
[00379] Step e: 2-(7-Methoxybenzo[d] [1 ,3]dioxol-5-yl)acetonitrile
To a solution of 6-(chloromethyl)-4-methoxybenzo[d][l,3]dioxole (10.2 g, 40 mmol) in DMSO (100 mL) was added NaCN (2.43 g, 50 mmol) at room temperature. The mixture was stirred for 3 h and poured into water (500 mL). The aqueous phase was extracted with EtOAc (100 mL x 3). The combined organic layers were dried over anhydrous Na2SO4 and evaporated to give the crude product, which was washed with ether to afford 2-(7- methoxybenzo[d][l,3]dioxol-5-yl)acetonitrile (4.6 g, 45%). 1H NMR (400 MHz, CDCl3) δ 6.49 (s, 2 H), 5.98 (s, 2 H), 3.91 (s, 3 H), 3.65 (s, 2 H). 13C NMR (400 MHz, CDCl3) δ 148.9, 143.4, 134.6, 123.4, 117.3, 107.2, 101.8, 101.3, 56.3, 23.1.
J. 1 -(Benzofuran-5-yl)cvclopropanecarboxylic acid
Figure imgf000122_0001
[00380] Step a: l-[4-(2,2-Diethoxy-ethoxy)-phenyl]-cyclopropanecarboxylic acid
To a stirred solution of l-(4-hydroxy-phenyl)-cyclopropanecarboxylic acid methyl ester (15.0 g, 84.3 mmol) in DMF (50 mL) was added sodium hydride (6.7 g, 170 mmol, 60% in mineral oil) at 0 0C. After hydrogen evolution ceased, 2-bromo-l,l-diethoxy-ethane (16.5 g, 84.3 mmol) was added dropwise to the reaction mixture. The reaction was stirred at 160 0C for 15 hours. The reaction mixture was poured onto ice (100 g) and extracted with CH2Cl2. The combined organics were dried over Na2SO4. The solvent was evaporated under vacuum to give crude l-[4-(2,2-diethoxy-ethoxy)-phenyl]-cyclopropanecarboxylic acid (10 g), which was used directly in the next step without purification.
[00381] Step b: l-Benzofuran-5-yl-cycloproρanecarboxylic acid
Figure imgf000123_0001
of crude H4-(2,2<Ue<hoxy-e<hoxy)-ptayI]- cyclopropanecarboxylic acid (20 g, -65 mmol) in xylene (100 mL) was added PPA (22.2 g, 64.9 mmol) at room temperature. The mixture was heated at reflux (140 0C) for 1 hour before it was cooled to room temperature and decanted from the PPA. The solvent was evaporated under vacuum to obtain the crude product, which was purified by preparative HPLC to provide l-(benzofuran-5-yl)cyclopropanecarboxylic acid (1.5 g, 5%). 1H NMR (400 MHz, DMSCM6) δ 12.25 (br s, 1 H), 7.95 (d, J = 2.8 Hz, 1 H), 7.56 (d, J= 2.0 Hz, 1 H), 7.47 (d, J= 11.6 Hz, 1 H), 7.25 (dd, J= 2.4, 11.2 Hz, 1 H), 6.89 (d, J= 1.6 Hz, 1 H), 1.47-1.44 (m, 2 H), 1.17-1.14 (m, 2 H).
K. l-(2,3-Dihvdrobenzofuran-5-yl)cvclopropanecarboxylic acid
Figure imgf000123_0002
[00382] To a solution of l-(benzofuran-5-yl)cyclopropanecarboxylic acid (700 mg, 3.47 mmol) in MeOH (10 mL) was added PtO2 (140 mg, 20%) at room temperature. The stirred reaction mixture was hydrogenated under hydrogen (1 atm) at 10 °C for 3 days. The reaction mixture was filtered. The solvent was evaporated under vacuum to afford the crude product, which was purified by preparative HPLC to give l-(2,3-dihydrobenzofuran-5- yl)cyclopropanecarboxylic acid (330 mg, 47%). 1H NMR (400 MHz, CDCl3) δ 7.20 (s, 1 H), 7.10 (d, J= 10.8 Hz, 1 H), 6.73 (d, J= 11.2 Hz, 1 H), 4.57 (t, J= 11.6 Hz, 2 H), 3.20 (t, J= 11.6 Hz, 2H), 1.67-1.63 (m, 2 H), 1.25-1.21 (m, 2 H).
L. 2-(2,2-Dimethylbenzo|"d][1.31dioxol-5-vDacetonitrile
BBr31 DCM
Figure imgf000123_0003
Figure imgf000123_0004
[00383] Step a: (3,4-Dihydroxy-ρhenyl)-acetonitrile
To a solution of benzo[l,3]dioxol-5-yl-acetonitrile (0.50 g, 3.1 mmol) in CH2Cl2 (15 mL) was added dropwise BBr3 (0.78 g, 3.1 mmol) at -78 0C under N2. The mixture was slowly warmed to room temperature and stirred overnight. H2O (10 mL) was added to quench the reaction and the CH2Cl2 layer was separated. The aqueous phase was extracted with CH2Cl2 (2 x 7 mL). The combined organics were washed with brine, dried over Na2SO4 and purified by column chromatography on silica gel (Petroleum Ether/EtOAc 5:1) to give (3,4-dihydroxy- > c T p/he uny sϊ)- Qac eeto /ni>triore ( s0:2e5 « g3, 54%) as a white solid. 1H NMR (DMSO-J6, 400 MHz) δ 9.07 (s, 1 H), 8.95 (s, 1 H), 6.68-6.70 (m, 2 H), 6.55 (dd, J = 8.0, 2.0 Hz, 1 H), 3.32 (s, 2 H).
[00384] Step b: 2-(2,2-Dimethylbenzo[d][l,3]dioxol-5-yl)acetonitrile
To a solution of (3,4-dihydroxy-phenyl)-acetonitiile (0.2 g, 1.3 mmol) in toluene (4 mL) was added 2,2-dimethoxy-propane (0.28 g, 2.6 mmol) and TsOH (0.010 g, 0.065 mmol). The mixture was heated at reflux overnight. The reaction mixture was evaporated to remove the solvent and the residue was dissolved in ethyl acetate. The organic layer was washed with NaHCO3 solution, H2O, brine, and dried over Na2SO4. The solvent was evaporated under reduced pressure to give a residue, which was purified by column chromatography on silica gel (Petroleum Ether/EtO Ac 10:1) to give 2-(2,2-dimethylbenzo[d][l,3]dioxol-5-yl)acetonitrile (40 mg, 20%). 1H NMR (CDCl3, 400 MHz) δ 6.68-6.71 (m, 3 H), 3.64 (s, 2 H), 1.67 (s, 6 H).
M. 2-(3-(Benzyloxy)-4-chlorophenvDacetonitrile
Figure imgf000124_0001
[00385] Step a: (4-Chloro-3-hydroxy-phenyl)acetonitrile
BBr3 (16.6 g, 66 mmol) was slowly added to a solution of 2-(4-chloro-3- methoxyphenyl)acetonitrile (12 g, 66 mmol) in DCM (120 mL) at -78 0C under N2. The reaction temperature was slowly increased to room temperature. The reaction mixture was stirred overnight and then poured into ice and water. The organic layer was separated, and the aqueous layer was extracted with DCM (40 mL x 3). The combined organic layers were washed with water, brine, dried over Na2SO4, and concentrated under vacuum to give (4-chloro- 3-hydroxy-phenyl)-acetonitrile (9.3 g, 85%). 1H NMR (300 MHz, CDCl3) δ 7.34 (d, J = 8.4 Hz, 1 H), 7.02 (d, J = 2.1 Hz, 1 H), 6.87 (dd, J = 2.1, 8.4 Hz, 1 H), 5.15 (brs, IH), 3.72 (s, 2 H).
[00386] Step b: 2-(3-(Benzyloxy)-4-chlorophenyl)acetonitrile
To a solution of (4-chloro-3-hydroxy-phenyl)acetonitrile (6.2 g, 37 mmol) in CH3CN (80 mL) was added K2CO3 (10.2 g, 74 mmol) and BnBr (7.6 g, 44 mmol). The mixture was stirred at room temperature overnight. The solids were filtered off and the filtrate was evaporated under vacuum. The residue was purified by column chromatography on silica gel (Petroleum Ether/Ethyl Acetate 50:1) to give 2-(3-(benzyloxy)-4-chlorophenyl)acetonitrile (5.6
Figure imgf000125_0001
J = 2 Hz, 2 H), 6.86 (dd, J = 2.0, 8.4 Hz, 1 H), 5.18 (s, 2 H), 3.71 (s, 2 H).
N. 2-(Quinoxalin-6-yl)acetonitrile
Figure imgf000125_0002
[00387] Step a: 6-Methylquinoxaline
To a solution of 4-methylbenzene-l,2-diamine (50.0 g, 0.41 mol) in isopropanol (300 mL) was added a solution of glyoxal (40% in water, 65.3 g, 0.45 mol) at room temperature. The reaction mixture was heated at 80 °C for 2 hours and evaporated under vacuum to give 6-methylquinoxaline (55 g, 93%), which was used directly in the next step. 1H NMR (300 MHz, CDCl3) δ 8.77 (dd, J = 1.5, 7.2 Hz, 2 H), 7.99 (d, J = 8.7 Hz, 1 H), 7.87 (s, 1 H), 7.60 (dd, J = 1.5, 8.4 Hz, 1 H), 2.59 (s, 3 H).
[00388] Step b: 6-Bromomethylquinoxaline
To a solution of 6-methylquinoxaline (10.0 g, 69.4 mmol) in CCl4 (80 mL) was added NBS (13.5 g, 76.3 mmol) and benzoyl peroxide (BP, 1.7 g, 6.9 mmol) at room temperature. The mixture was heated at reflux for 2 hours. After cooling, the mixture was evaporated under vacuum to give a yellow solid, which was extracted with Petroleum Ether (50 mL x 5). The extracts were concentrated under vacuum. The organics were combined and concentrated to give crude 6-bromomethylquinoxaline (12.0 g), which was used directly in the next step. 1H NMR (300 MHz, CDCl3) δ 8.85-8.87 (m, 2 H), 8.10-8.13 (m, 2 H), 7.82 (dd, J = 2.1, 8.7 Hz, I H), 4.70 (s, 2 H).
[00389] Step c: 2-(Quinoxalin-6-yl)acetonitrile
To a solution of crude 6-bromomethylquinoxaline (36.0 g) in 95% ethanol (200 mL) was added NaCN (30.9 g, 0.63 mol) at room temperature. The mixture was heated at 50 0C for 3 hours and then concentrated under vacuum. Water (100 mL) and ethyl acetate (100 mL) were added. The organic layer was separated and the aqueous layer was extracted with ethyl acetate. The combined organics were washed with brine, dried over Na2SO4 and concentrated under vacuum. The residue was purified by silica gel column (Petroleum Ether/EtOAc 10:1) to give !P C 'T'./1 Il B Q B S «■!■ H P H «ϊ ,
2-(quinoxalin-6-yl)acetbnitrile (7.9 g, 23% over two steps). 1H NMR (300 MHz, CDCl3) δ
8.88-8.90 (m, 2 H), 8.12-8.18 (m, 2 H), 7.74 (dd, J = 2.1, 8.7 Hz, 1 H), 4.02 (s, 2 H). MS (ESI) m/z (M+H)+ 170.0.
O. 2-(Ouinolin-6-yl)acetom'trile
Figure imgf000126_0001
[00390] Step a: 6-Bromomethylquinoline
To a solution of 6-methylquinoline (2.15 g, 15.0 mmol) in CCl4 (30 mL) was added NBS (2.92 g, 16.5 mmol) and benzoyl peroxide (BP, 0.36 g, 1.5 mmol) at room temperature. The mixture was heated at reflux for 2 hours. After cooling, the mixture was evaporated under vacuum to give a yellow solid, which was extracted with Petroleum Ether (30 mL x 5). The extracts were concentrated under vacuum to give crude 6-bromomethylquinoline (1.8 g), which was used directly in the next step.
[00391] Step b: 2-(Qumolin-6-yl)acetonitrile
To a solution of crude 6-bromomethylquinoline (1.8 g) in 95% ethanol (30 mL) was added NaCN (2.0 g, 40.8 mmol) at room temperature. The mixture was heated at 50 °C for 3 hours and then concentrated under vacuum. Water (50 mL) and ethyl acetate (50 mL) were added. The organic layer was separated and the aqueous layer was extracted with ethyl acetate. The combined organics were washed with brine, dried over Na2SO4 and concentrated under vacuum. The combined crude product was purified by column (Petroleum Ether /EtOAc 5:1) to give 2-(quinolin-6-yl)acetonitrile (0.25 g, 8% over two steps). 1H NMR (300 MHz, CDCl3) δ 8.95 (dd, J = 1.5, 4.2 Hz, 1 H), 8.12-8.19 (m, 2 H), 7.85 (s, 1 H), 7.62 (dd, J = 2.1, 8.7 Hz, 1 H), 7.46 (q, J = 4.2 Hz, 1 H), 3.96 (s, 2 H). MS (ESI) m/e (M+H)+ 169.0.
P. 2-(2,3-DihvdrobenzorbirL41dioxm-6-vnacetonitrile
Figure imgf000127_0001
Figure imgf000127_0002
[00392] Step a: 2,3-Dihydro~benzo[l,4]dioxine-6-carboxylic acid ethyl ester
To a suspension of Cs2CO3 (270 g, 1.49 mol) in DMF (1000 mL) were added 3,4- dihydroxybenzoic acid ethyl ester (54.6 g, 0.3 mol) and 1,2-dibromoethane (54.3 g, 0.29 mol) at room temperature. The resulting mixture was stirred at 80 0C overnight and then poured into ice-water. The mixture was extracted with EtOAc (200 mL x 3). The combined organic layers were washed with water (200 mL x 3) and brine (100 mL), dried over Na2SO4 and concentrated to dryness. The residue was purified by column (Petroleum Ether /Ethyl Acetate 50:1) on silica gel to obtain 2,3-dihydro-benzo[l,4]dioxine-6-carboxylic acid ethyl ester (18 g, 29%). 1H NMR (300 MHz, CDCl3) δ 7.53 (dd, J = 1.8, 7.2 Hz, 2 H), 6.84-6.87 (m, 1 H), 4.22-4.34 (m, 6 H), 1.35 (t, J = 7.2 Hz, 3 H).
[00393] Step b: (2,3-Dihydro-benzo[l,4]dioxm-6-yl)-methanol
To a suspension of LAH (2.8 g, 74 mmol) in THF (20 mL) was added dropwise a solution of 2,3-dihydro-benzo[l,4]dioxine-6-carboxylic acid ethyl ester (15 g, 72 mmol) in THF (10 mL) at 0 °C under N2. The mixture was stirred at room temperature for 1 h and then quenched carefully with addition of water (2.8 mL) and NaOH (10%, 28 mL) with cooling. The precipitated solid was filtered off and the filtrate was evaporated to dryness to obtain (2,3- dihydro-benzo[l,4]dioxin-6-yl)-methanol (10.6 g). 1H NMR (300 MHz, DMSO-d6) δ 6.73-6.78 (m, 3 H), 5.02 (t, J = 5.7 Hz, 1 H), 4.34 (d, J = 6.0 Hz, 2 H), 4.17-4.20 (m, 4 H).
[00394] Step c: 6-Chloromethyl-2,3-dihydro-benzo[l,4]dioxine
A mixture of (2,3-dihydro-benzo[l,4]dioxin-6-yl)methanol (10.6 g) in SOCl2 (10 mL) was stirred at room temperature for 10 min and then poured into ice-water. The organic layer was separated and the aqueous phase was extracted with dichloromethane (50 mL x 3). The combined organic layers were washed with NaHCO3 (sat solution), water and brine, dried over NaaSO4 and concentrated to dryness to obtain 6-chloromethyl-2,3-dihydro- benzo[l,4]dioxine (12 g> 88% over two steps), which was used directly in next step.
[00395] Step d: 2-(2,3-Dihydrobenzo[b][l,4]dioxin-6-yl)acetonitrile A mixture of 6-chloromethyl-2,3-dihydro-benzo[l,4]dioxine (12.5 g, 67.7 mmol) and NaCN (4.30 g, 87.8 mmol) in DMSO (50 mL) was stirred at rt for 1 h. The mixture was poured into water (150 mL) and then extracted with dichloromethane (50 mL x 4). The combined organic layers were washed with water (50 mL x 2) and brine (50 mL), dried over Na2SO4 and concentrated to dryness. The residue was purified by column (Petroleum Ether/Ethyl Acetate 50:1) on silica gel to obtain 2-(2,3-dihydrobenzo[b][l,4]dioxin-6- yl)acetonitrile as a yellow oil (10.2 g, 86%). 1H-NMR (300 MHz, CDCl3) δ 6.78-6.86 (m, 3 H), 4.25 (s, 4 H), 3.63 (s, 2 H).
Q. 2-(2,2.4,4-Tetrafluoro-4H-benzo[d1 f 1.31dioxm-6-vDacetonitrile
Figure imgf000128_0001
SOCIp
Figure imgf000128_0002
[00396] Step a: 2,2,4,4-Tetrafluoro-4H-benzo[l,3]dioxine-6-carboxylic acid methyl ester
A suspension of 6-bromo-2,2,4,4~tetrafluoro-4H-benzo[l,3]dioxine (4.75 g, 16.6 mmol) and Pd(PPh3)4 (950 mg, 8.23 mmol) in MeOH (20 mL), MeCN (30 mL) and Et3N (10 mL) was stirred under carbon monoxide atmosphere (55 psi) at 75 °C (oil bath temperature) overnight. The cooled reaction mixture was filtered and the filtrate was concentrated. The residue was purified by silica gel column (Petroleum Ether) to give 2,2,4,4-tetrafluoro-4H- benzo[l,3]dioxine-6-carboxylic acid methyl ester (3.75 g, 85%). 1H NMR (CDCl3, 300 MHz) δ 8.34 (s, 1 H), 8.26 (dd, J = 2.1, 8.7 Hz, 1 H), 7.22 (d, J = 8.7 Hz, 1 H), 3.96 (s, 3 H).
[00397] Step b: (2,2,4,4-Tetrafluoro-4H-benzo[l,3]dioxin-6-yl)methanol
To a suspension of LAH (2.14 g, 56.4 mmol) in dry THF (200 mL) was added dropwise a solution of 2,2,4 ,4-tetrafluoro-4H-benzo[l,3]dioxine-6-carboxylic acid methyl ester (7.50 g, 28.2 mmol) in dry THF (50 mL) at 0 0C. After being stirred at 0 °C for 1 h, the reaction mixture was treated with water (2.14 g) and 10% NaOH (2.14 mL). The slurry was filtered and washed with THF. The combined filtrates were evaporated to dryness to give the crude (2,2,4,4-tetrafluoro-4H-benzo[l,3]dioxin-6-yl)-methanol (6.5 g), which was used directly in the
- ITJ - . ' next step. 1H NM [CDbI3, 300 MHz) δ 7.64 (s, 1 H), 7.57-7.60 (m, 1 H), 7.58 (d, J = 8.7 Hz, 1 H), 4.75 (s, 2 H).
[00398] Step c: 6-Chloromethyl-2,2,4,4-tetrafluoro-4H-benzo[l,3]dioxine
A mixture of (2,2,4,4-tetrafluoro-4H-benzo[l,3]dioxin-6-yl)-methanol (6.5 g) in thionyl chloride (75 mL) was heated at reflux overnight. The resulting mixture was concentrated under vacuum. The residue was basified with aqueous saturated NaHCO3. The aqueous layer was extracted with dichloromethane (50 mL x 3). The combined organic layers were dried over Na2SO4, filtrated, and concentrated under reduced pressure to give 6- chloromethyl-2,2,4,4-tetrafluoro-4H-benzo[l,3]dioxine (6.2 g), which was used directly in the next step. 1H NMR (CDCl3, 300 MHz) δ 7.65 (s, 1 H), 7.61 (dd, J = 2.1, 8.7 Hz, 1 H), 7.15 (d, J = 8.4 Hz, 1 H), 4.60 (s, 2 H).
[00399] Step d: (2,2,4,4-Tetrafluoro-4H-benzo[l,3]dioxin-6-yl)-acetonitrile
A mixture of 6-chloromethyl-2,2,4,4-tetrafluoro-4H-benzo[l,3]dioxine (6.2 g) and NaCN (2.07 g, 42.3 mmol) in DMSO (50 mL) was stirred at room temperature for 2 h. The reaction mixture was poured into ice and extracted with EtOAc (50 mL x 3). The combined organic layers were dried over anhydrous Na2SO4, and evaporated to give a crude product, which was purified by silica gel column (Petroleum Ether/EtOAc 10:1) to give (2,2-difluoro- benzo[l,3]dioxol~5-yl)-acetonitrile (4.5 g, 68% over 3 steps). 1H NMR (CDCl3, 300 MHz) δ 7.57-7.60 (m, 2 H), 7.20 (d, J = 8.7 Hz, 1 H), 3.82 (s, 2 H).
R. 2-(4H-Benzofdl fL3]dioxin-7-yl)acetonitrile
Figure imgf000129_0001
[00400] Step a: (3-Hydroxyρhenyl)acetonitrile
To a solution of (3-methoxyρhenyl)acetonitrile (150 g, 1.03 mol) in CH2Cl2 (1000 mL) was added BBr3 (774 g, 3.09 mol) dropwise at -70 °C. The mixture was stirred and warmed to room temperature slowly. Water (300 mL) was added at 0 0C. The resulting mixture was extracted with CH2Cl2. The combined organic layers were dried over anhydrous Na2SO4, filtered, and evaporated under vacuum. The crude residue was purified by column (Petroleum Ether /EtOAc 10:1) to give (3-hydroxyphenyl)acetonitrile (75.0 g, 55%). 1H NMR (CDCl3, 300 MHz) δ 7.18-7.24 (m, 1 H), 6.79-6.84 (m, 3 H), 3.69 (s, 2 H).
[00401] Step b: 2-(4H-Benzo[d] [1 ,3]dioxin-7-yl)acetonitrile To a solution of (3-hydroxyphenyl)acetonitrile (75.0 g, 0.56 mol) in toluene (750 mL) was added paraformaldehyde (84.0 g, 2.80 mol) and toluene-4-sulfonic acid monohydrate (10.7 g, 56.0 mmol) at room temperature. The reaction mixture was heated at reflux for 40 minutes. Toluene was removed by evaporation. Water (150 mL) and ethyl acetate (150 mL) were added. The organic layer was separated and the aqueous layer was extracted with ethyl acetate. The combined organics were washed with brine, dried over anhydrous Na2SO4 and evaporated under vacuum. The residue was separated by preparative HPLC to give 2-(4H- benzo[d][l,3]dioxin-7-yl)acetonitrile (4.7 g, 5%). 1H NMR (300 MHz, CDCl3) δ 6.85-6.98 (m, 3 H), 5.25 (d, J = 3.0 Hz, 2 H), 4.89 (s, 2 H), 3.69 (s, 2 H).
S. 2-f4H-Benzofd1 [T ,31dioxin-6-vDacetonitrile
paraformaldehyde
Figure imgf000130_0001
toluene
Figure imgf000130_0002
[00402] To a solution of (4-hydroxyρhenyl)acetonitrile (17.3 g, 0.13 mol) in toluene (350 mL) were added paraformaldehyde (39.0 g, 0.43 mmol) and toluene-4-sulfonic acid monohydrate (2.5 g, 13 mmol) at room temperature. The reaction mixture was heated at reflux for 1 hour. Toluene was removed by evaporation. Water (150 mL) and ethyl acetate (150 mL) were added. The organic layer was separated and the aqueous layer was extracted with ethyl acetate. The combined organics were washed with brine, dried over Na2SO4 and evaporated under vacuum. The residue was separated by preparative HPLC to give 2-(4H- benzo[d][l,3]dioxin-6-yl)acetonitrile (7.35 g, 32%). 1HNMR (400 MHz, CDCl3) δ 7.07-7.11 (m, 1 H), 6.95-6.95 (m, 1 H), 6.88 (d, J = 11.6 Hz, 1 H), 5.24 (s, 2 H), 4.89 (s, 2 H), 3.67 (s, 2 H).
T. 2-(3-(Benzyloxy)-4-methoxyphenyl)acetonitrile
Figure imgf000130_0003
[00403] To a suspension of t-BuOK (20.15 g, 0.165 mol) in THF (250 mL) was added a solution of TosMIC (16.1 g, 82.6 mmol) in THF (100 mL) at -78 °C. The mixture was stirred for 15 minutes, treated with a solution of 3-benzyloxy-4-methoxy-benzaldehyde (10.0 g, P C T / '5I1.X9 S MGoEfLy/fn y fO ϊBϊFl1;i:(5Sϋ!rSαL) dropwise, and continued to stir for 1.5 hours at -78 0C. To the cooled reaction mixture was added methanol (50 mL). The mixture was heated at reflux for 30 minutes. Solvent of the reaction mixture was removed to give a crude product, which was dissolved in water (300 mL). The aqueous phase was extracted with EtOAc (100 mL x 3). The combined organic layers were dried and evaporated under reduced pressure to give crude product, which was purified by column chromatography (Petroleum Ether/EtOAc 10:1) to afford 2-(3-(Benzyloxy)-4-methoxyphenyl)acetonitril (5.0 g, 48%). 1H NMR (300 MHz, CDCl3) δ 7.48-7.33 (m, 5 H), 6.89-6.86 (m, 3 H), 5.17 (s, 2 H), 3.90 (s, 3 H), 3.66 (s, 2 H). 13C NMR (75 MHz, CDCl3) δ 149.6, 148.6, 136.8, 128.8, 128.8, 128.2, 127.5, 127.5, 122.1, 120.9, 118.2, 113.8, 112.2, 71.2, 56.2, 23.3.
[00404] The following Table 2 contains a list of carboxylic acid building blocks that were commercially available, or prepared by one of the methods described above:
[00405] Table 2: Carboxylic acid building blocks.
Figure imgf000131_0001
Figure imgf000132_0002
U. 6-Chloro-5-methvIpyridm-2-amme
Figure imgf000132_0001
[00406] Step a: 2,2-Dimethyl-N-(5-methyl-pyridin-2-yl)-ρroρionarnide
To a stirred solution of 5-memylpyridin-2-arnine (200 g, 1.85 mol) in anhydrous CH2Cl2 (1000 mL) was added dropwise a solution Of Et3N (513 mL, 3.70 mol) and 2,2- dimethyl-propionyl chloride (274 mL, 2.22 mol) at 0 0C under N2. The ice bath was removed and stirring was continued at room temperature for 2 hours. The reaction was poured into ice (2000 g). The organic layer was separated and the remaining aqueous layer was extracted with CH2Cl2 (3x). The combined organics were dried over Na2SO4 and evaporated to afford 2,2- dimethyl-JV-(5-methyl-pyridin-2-yl)-propionamide (350 g), which was used in the next step without further purification. 1H NMR (400 MHz, CDCl3) δ 8.12 (d, /= 8.4 Hz, 1 H), 8.06 (d, J = 1.2 Hz, 1 H), 7.96 (s, 1 H), 7.49 (dd, /= 1.6, 8.4 Hz, 1 H), 2.27 (s, 1 H), 1.30 (s, 9 H).
[00407] Step b: 2,2-Dimethyl-7Y-(5-methyl-l-oxy-pyridin-2-yl)-propionamide
To a stirred solution of 2,2-dimethyl-N-(5-methyl-pyridin-2-yl)-ρropionamide (100 g, 0.52 mol) in AcOH (500 mL) was added drop-wise 30% H2O2 (80 mL, 2.6 mol) at room temperature. The mixture was stirred at 80 0C for 12 hours. The reaction mixture was evaporated under vacuum to obtain 2,2-dimethyl-jV~(5-methyl~l-oxy-pyridin-2-yl)- propionamide (80 g, 85% purity). 1H NMR (400 MHz, CDCl3) δ 10.26 (br s, 1 H), 8.33 (d, J = 8.4 Hz, 1 H), 8.12 (s, 1 H), 7.17 (dd, J = 0.8, 8.8 Hz, 1 H), 2.28 (s, 1 H), 1.34 (s, 9 H).
[00408] Step c: N-(6-Chloro-5-methyl-pyridin-2-yl)-2,2-dimethyl-propionamide
To a stirred solution of 2,2-dimethyl-N-(5-methyl-l-oxy-pyridin-2-yl)-propionamide (10 g, 48 mmol) in anhydrous CH2Cl2 (50 mL) was added Et3N (60 mL, 240 mmol) at room temperature. After being stirred for 30 min, POCl3 (20 mL) was added drop-wise to the reaction mixture. The reaction was stirred at 50 0C for 15 hours. The reaction mixture was poured into ice (200 g). The organic layer was separated and the remaining aqueous layer was extracted with CH2Cl2 (3x). The combined organics were dried over Na2SO4. The solvent was evaporated under vacuum to obtain the crude product, which was purified by chromatography (Petroleum Ether/EtOAc 100:1) to provide N-(6-chloro-5-methyl-pyridin-2-yl)- 2,2-dimethyl- propionamide (0.5 g, 5%). 1H NMR (400 MHz, CDCl3) δ 8.09 (d, J - 8.0 Hz, 1 H), 7.94 (br s, 1 H), 7.55 (d, / = 8.4 Hz, 1 H), 2.33 (s, 1 H), 1.30 (s, 9 H).
[00409] Step d: 6-Chloro-5-methyl-ρyridin-2-ylamine
To N-(6-chloro-5-methyl-pyridin-2-yl)- 2,2-dimethyl-propionamide (4.00 g, 17.7 mmol) was added 6 N HCl (20 mL) at room temperature. The mixture was stirred at 80 0C for 12 hours. The reaction mixture was basified with drop-wise addition of sat. NaHCO3 to pH 8-9, and then the mixture was extracted with CH2Cl2 (3x). The organic phases were dried over Na2SO4 and evaporated under vacuum to obtain the 6-chloro-5-methyl-pyridin-2-ylamine (900 mg, 36%). 1H NMR (400 MHz, CDCl3) δ 7.28 (d, /= 8.0 Hz, 1 H), 6.35 (d, /= 8.0 Hz, 1 H), 4.39 (br s, 2 H), 2.22 (s, 3 H). MS (ESI) m/z: 143 (M-I-H+).
V. 6-Chloro-5-(trifluoromethyl)pyridin-2-amine
Figure imgf000133_0001
[00410] 2,6-Dichloro-3-(trifluoromethyl)pyridine (5.00 g, 23.2 mmol) and 28% aqueous ammonia (150 mL) were placed in a 250 mL autoclave. The mixture was heated at 93 0C for 21h. The reaction was cooled to rt and extracted with EtOAc (100 mL x 3). The combined organic extracts were dried over anhydrous Na2SO4 and evaporated under vacuum to give the crude product, which was purified by column chromatography on silica gel (2-20% EtOAc in petroleum ether as eluant) to give 6-chloro-5-(trifluoromethyl)pyridin-2-amine (2.1 g, 46% yield). 1H NMR (400 MHz, DMSO-J6) δ 7.69 (d, J = 8.4 Hz, 1 H), 7.13 (br s, 2 H), 6.43 (d, J = 8.4 Hz, 1 H). MS (ESI) m/z (M + H)+ 197.2
General Procedure IV; Coupling Reactions
Figure imgf000134_0001
Hal = Cl, Br, I, all other variables. Ring A is the ring formed by R3 and R'3. X = C or N
[00411] One equivalent of the appropriate carboxylic acid was placed in an oven- dried flask under nitrogen. Thionyl chloride (3 equivalents) and a catalytic amount of N,N- dimethylformamide was added and the solution was allowed to stir at 60 0C for 30 minutes. The excess thionyl chloride was removed under vacuum and the resulting solid was suspended in a minimum of anhydrous pyridine. This solution was slowly added to a stirred solution of one equivalent the appropriate aminoheterocycle dissolved in a minimum of anhydrous pyridine. The resulting mixture was allowed to stir for 15 hours at 110 0C. The mixture was evaporated to dryness, suspended in dichloromethane, and then extracted three times with IN NaOH. The organic layer was then dried over sodium sulfate, evaporated to dryness, and then purified by column chromatography.
W. l-(BenzordirL31dioxol-5-yl)-iV-(5-bromopyridin-2-yl)cyclopropane-carboxamide (B-I)
Figure imgf000134_0002
[00412] l-Benzo[l,3]dioxol-5-yl-cyclopropanecarboxylic acid (2.38 g, 11.5 mmol) was placed in an oven-dried flask under nitrogen. Thionyl chloride (2.5 mL) and N,N- dimethylformamide (0.3 mL) were added and the solution was allowed to stir for 30 minutes at 600C. The excess thionyl chloride was removed under vacuum and the resulting solid was suspended in 7 mL of anhydrous pyridine. This solution was then slowly added to a solution of 5-bromo-pyridin-2-ylamine (2.00 g, 11.6 mmol) suspended in 10 mL of anhydrous pyridine. The resulting mixture was allowed to stir for 15 hours at 110 0C. The mixture was then evaporated to dryness, suspended in 100 mL of dichloromethane, and washed with three 25 mL portions of IN NaOH. The organic layer was dried over sodium sulfate, evaporated to near dryness, and then purified by silica gel column chromatography utilizing dichloromethane as the eluent to yield the pure product (3.46 g, 83%) ESI-MS m/z calc. 361.2, found 362.1 (M+l)+; Retention time 3.40 minutes. 1H NMR (400 MHz, DMSO-J6) δ 1.06-1.21 (m, 2H), 1.44-1.51 (m, 2H), 6.07 (s, 2H), 6.93-7.02 (m, 2H), 7.10 (d, /= 1.6 Hz, IH), 8.02 (d, J= 1.6 Hz, 2H), 8.34 (s, IH), 8.45 (s, IH).
X. l-(Benzor(firi,31dioxol-6-yl)-iV-(6-bromopyridin-2-yl)cyclopropane-carboxamide (B-2)
Figure imgf000135_0001
[00413] (l-Benzo[l,3]dioxol-5-yl-cycloρropanecarboxylic acid (1.2 g, 5.8 mmol) was placed in an oven-dried flask under nitrogen. Thionyl chloride (2.5 mL) and N1N- dimethylformamide (0.3 mL) were added and the solution was allowed to stir at 60 0C for 30 minutes. The excess thionyl chloride was removed under vacuum and the resulting solid was suspended in 5 mL of anhydrous pyridine. This solution was then slowly added to a solution of 6-bromopyridin-2-amine (1.0 g, 5.8 mmol) suspended in 10 mL of anhydrous pyridine. The resulting mixture was allowed to stir for 15 hours at 110 0C. The mixture was then evaporated to dryness, suspended in 50 mL of dichloromethane, and washed with three 20 mL portions of IN NaOH. The organic layer was dried over sodium sulfate, evaporated to near dryness, and then purified by silica gel column chromatography utilizing dichloromethane containing 2.5 % triethylamine as the eluent to yield the pure product. ESI-MS m/z calc. 361.2, found 362.1 (M+l)+; Retention time 3.43 minutes. 1H NMR (400 MHz, DMSO-J5) δ 1.10-1.17 (m, 2H), 1.42-1.55 (m, 2H), 6.06 (s, 2H), 6.92-7.02 (m, 2H), 7.09 (d, J = 1.6 Hz, IH), 7.33 (d, J = 7.6 Hz, IH), 7.73 (t, J = 8.0 Hz, IH), 8.04 (d, J= 8.2 Hz, IH), 8.78 (s, IH).
[00414] The compounds in the following Table 3 were prepared in a manner analogous to that described above:
[00415] Table 3: Exemplary compounds synthesized according to Preparations W and X.
Figure imgf000135_0002
Figure imgf000136_0001
Figure imgf000137_0001
General Procedure V: Compounds of Formula I
Figure imgf000138_0001
Hal = Cl, Br, I. Ring A is the ring formed by R3 and R'3.
[00416] The appropriate aryl halide (1 equivalent) was dissolved in 1 mL of N,N- dimethylformamide (DMF) in a reaction tube. The appropriate boronic acid (1.3 equivalents), 0.1 mL of an aqueous 2 M potassium carbonate solution (2 equivalents), and a catalytic amount of Pd(dppf)Cl2 (0.09 equivalents) were added and the reaction mixture was heated at 80 0C for three hours or at 150 °C for 5 min in the microwave. The resulting material was cooled to room temperature, filtered, and purified by reverse-phase preparative liquid chromatography.
Y. l-Benzoπ,31dioxol-5-yl-cyclopropanecarboxylic acid r5-(2.4-dimethoxy-phenylV pyridin-2-vπ -amide
Figure imgf000138_0002
[00417] l-Benzo[l,3]dioxol-5-yl-cyclopropanecarboxylic acid (5-bromo-pyridin-
2-yi)-amide (36.1 mg, 0.10 mmol) was dissolved in 1 mL of iV,iV-dimethylfoπnamide in a reaction tube. 2,4-Dimethoxybenzeneboronic acid (24 mg, 0.13 mmol), 0.1 mL of an aqueous 2 M potassium carbonate solution, and a catalytic amount of Pd(dppf)Cl2 (6.6 mg, 0.0090 mmol) were added and the reaction mixture was heated at 80 0C for three hours. The resulting material was cooled to room temperature, filtered, and purified by reverse-phase preparative liquid chromatography to yield the pure product as a trifluoroacetic acid salt. ESI-MS m/z calc. 418.2, found 419.0 (M+l)+. Retention time 3.18 minutes. 1H NMR (400 MHz, CD3CN) δ 1.25-1.29 (m, 2H), 1.63-1.67 (m, 2H), 3.83 (s, 3H), 3.86 (s, 3H), 6.04 (s, 2H), 6.64-6.68 (m, 2H), 6.92 (d, J = 8.4 Hz, IH), 7.03-7.06 (m, 2H), 7.30 (d, /= 8.3 Hz, IH), 7.96 (d, J= 8.9 Hz, IH), 8.14 (dd, J= 8.9, 2.3 Hz, IH), 8.38 (d, J= 2.2 Hz, IH), 8.65 (s, IH). Z. 1 -Benzo [ 1 ,31dioxol-5-yl-cyclopropanecarboxylic acid r6-(4-dimethylamino-phenyl)- p yridin-2-yll -amide
Figure imgf000139_0001
[00418] l-Benzo[l,3]dioxol-5-yl-cyclopropanecarboxylic acid (6-bromo-pyridin-
2-yl)-amide (36 mg, 0.10 mmol) was dissolved in 1 mL of N,N-dimethylformamide in a reaction tube. 4-(Dimethylamino)phenylboronic acid (21 mg, 0.13 mmol), 0.1 mL of an aqueous 2 M potassium carbonate solution, and (Pd(dppf)Cl2 (6.6 mg, 0.0090 mmol) were added and the reaction mixture was heated at 80 0C for three hours. The resulting material was cooled to room temperature, filtered, and purified by reverse-phase preparative liquid chromatography to yield the pure product as a trifluoroacetic acid salt. ESI-MS m/z calc. 401.2, found 402.5 (M+l)+. Retention time 2.96 minutes. 1H NMR (400 MHz, CD3CN) δ 1.23-1.27 (m, 2H), 1.62-1.66 (m, 2H), 3.04 (s, 6H), 6.06 (s, 2H), 6.88-6.90 (m, 2H), 6.93-6.96 (m, IH), 7.05-7.07 (m, 2H), 7.53- 7.56 (m, IH), 7.77-7.81 (m, 3H), 7.84-7.89 (m, IH), 8.34 (s, IH).
[00419] The following schemes were utilized to prepare additional boronic esters which were not commercially available:
AA. l-Methyl-4-r4-(4.4.5.5-tetramethyl-L3,2-dioxaborolan-2-vDphenyll- sulfonylpiperazine
Figure imgf000139_0002
[00420] Step a: l-(4-Bromophenylsulfonyl)-4-methylpiperazine
A solution of 4-bromobenzene-l-sulfonyl chloride (256 mg, 1.00 mmol) in 1 mL of dichloromethane was slowly added to a vial (40 mL) containing 5 mL of a saturated aqueous solution of sodium bicarbonate, dichloromethane (5 mL) and 1-methylpiperazine (100 mg, 1.00 mmol). The reaction was stirred at room temperature overnight. The phases were separated and the organic layer was dried over magnesium sulfate. Evaporation of the solvent under reduced pressure provided the required product, which was used in the next step without further purification. ESI-MS m/z calc. 318.0, found 318.9 (M+l)+. Retention time of 1.30 minutes. 1H 'VIJ S O S /'4312 B l!3 . NMR (300 MHz, CDCl3) δ 7.65 (d, J= 8.7 Hz, 2H), 7.58 (d, /= 8.7 Hz, 2H), 3.03 (t, J = 4.2
Hz, 4H), 2.48 (t, J= 4.2 Hz, 4H), 2.26 (s, 3H).
[00421] Step b: l-Methyl-4-[4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2- yl)phenyl]sulfonyl-piperazine
A 50 mL round bottom flask was charged with l-(4-bromophenyl-sulfonyl)-4- methylpiperazine (110 mg, 0.350 mmol), &ιs-(pinacolato)-diboron (93 mg, 0.37 mmol), palladium acetate (6 mg, 0.02 mmol), and potassium acetate (103 mg, 1.05 mmol) in N,N- dimethylformamide (6 mL). The mixture was degassed by gently bubbling argon through the solution for 30 minutes at room temperature. The mixture was then heated at 80 0C under argon until the reaction was complete (4 hours). The desired product, l-methyl-4-[4-(4 ,4,5,5- tetramethyl-l,3,2-dioxaborolan-2-yl)phenyl]-sulfonyl-piperazine, and the bi-aryl product, 4-(4- methylpiperazin-l-ylsulfonyl)-phenyl-phenylsulfonyl-4-methylpiperazine, were obtained in a ratio of 1:2 as indicated by LC/MS analysis. The mixture was used without further purification.
BB. 4,4,5,5-Tetramethyl-2-(4-(2-('methylsulfonyl)ethyl)phenvD-l,3,2-dioxaborolane
Figure imgf000140_0001
[00422] Step a: 4-Bromophenethyl-4-methylbenzenesulfonate
To a 50 mL round-bottom flask was added p-bromophenethyl alcohol (1.0 g, 4.9 mmol), followed by the addition of pyridine (15 mL). To this clear solution was added, under argon, p-toluenesulfonyl chloride (TsCl) (1.4 g, 7.5 mmol) as a solid. The reaction mixture was purged with Argon and stirred at room temperature for 18 hours. The crude mixture was treated with IN HCl (20 mL) and extracted with ethyl acetate (5 x 25 mL). The organic fractions were dried over Na2SO4, filtered, and concentrated to yield 4-bromophenethyl-4- methylbenzenesulfonate (0.60 g, 35%) as a yellowish liquid. 1H-NMR (Acetone-^, 300 MHz) δ 7.64 (d, / = 8.4 Hz, 2H), 7.40-7.37 (d, / = 8.7 Hz, 4H), 7.09 (d, / = 8.5 Hz, 2H), 4.25 (t, / = 6.9 Hz, 2H), 2.92 (t, /= 6.3 Hz, 2H), 2.45 (s, 3H).
[00423] Step b: (4-Bromoρhenethyl)(methyl)sulfane
To a 20 mL round-bottom flask were added 4-bromophenethyl 4- methylbenzenesulfonate (0.354 g, 0.996 mmol) and CH3SNa (0.10 g, 1.5 mmol), followed by the addition of THF (1.5 mL) and iV-methyl-2-pyrrolidinone (1.0 mL). The mixture was stirred at room temperature for 48 hours, and then treated with a saturated aqueous solution of sodium bicarbonate (10 mL). The mixture was extracted with ethyl acetate (4 x 10 mL), dried over Na2SO4, filtered, and concentrated to yield (4-bromophenethyl)(methyl)sulfane (0.30 g crude) as a yellowish oil. 1H-NMR (CDCl3, 300 MHz) δ 7.40 (d, J = 8.4 Hz, 2H), 7.06 (d, J = 8.4 Hz, 2H), 2.89-2.81 (m, 2H), 2.74-2.69 (m, 2H), 2.10 (s, 3H).
[00424] Step c: l-Bromo-4-(2-methylsulfonyl)-ethylbenzene
To a 20 mL round-bottom flask were added (4-bromophenethyl)-(methyl)sulfane (0.311g, 1.34 mmol) and Oxone (3.1 g, 0.020 mol), followed by the addition of a 1:1 mixture of acetone/water (10 mL). The mixture was vigorously stirred at room temperature for 20 hours, before being concentrated. The aqueous mixture was extracted with ethyl acetate (3 x 15 mL) and dichloromethane (3 x 10 mL). The organic fractions were combined, dried with Na2SO4, filtered, and concentrated to yield a white semisolid. Purification of the crude material by flash chromatography yielded l-bromo-4-(2-methylsulfonyl)-ethylbenzene (0.283 g, 80%). 1H- NMR (DMSO-^5, 300 MHz) δ 7.49 (d, / = 8.4 Hz, 2H), 7.25 (d, J = 8.7 Hz, 2H), 3.43 (m, 2H), 2.99 (m, 2H), 2.97 (s, 3H).
[00425] Step d: 4,4,5, 5-Tetramethyl-2-(4-(2-(methylsulfonyl)ethyl)-phenyl)- 1,3,2- dioxaborolane
4,4,5,5-Tetramethyl-2-(4-(2-(methylsulfonyl)ethyl)ρhenyl)-l,3,2-dioxaborolane was prepared in the same manner as described above for l-memyl-4-[4-(4,4,5,5-tetramethyl-l,3,2- dioxaborolan-2-yl)phenyl]sulfonyl-piperazine, Preparation AA. CC. tert-Butyl methyl(4-(4,4.5.5-tetramethyl-l,3,2-dioxaborolan-2- vDbenzvπcarbamate
Figure imgf000142_0001
[00426] Step a: tert-Butyl-4-bromobenzylcarbamate
Commercially available p-bromobenzylarnine hydrochloride (1 g, 4 mmol) was treated with 10% aq. NaOH (5 mL). To the clear solution was added (Boc)2O (1.1 g, 4.9 mmol) dissolved in dioxane (10 mL). The mixture was vigorously stirred at room temperature for 18 hours. The resulting residue was concentrated, suspended in water (20 mL), extracted with ethyl acetate (4 x 20 mL), dried over Na2SO4, filtered, and concentrated to yield teτt-butyl-4- bromobenzylcarbamate (1.23 g, 96%) as a white solid. 1H NMR (300 MHz, OMSO-d6) δ 7.48 (d, J = 8.4 Hz, 2H), 7.40 (t, J = 6 Hz, IH), 7.17 (d, J = 8.4 Hz, 2H), 4.07 (d, J = 6.3 Hz, 2H), 1.38 (s, 9H).
[00427] Step b: tert-Butyl-4-bromobenzyl(methyl)carbamate
In a 60-mL vial, ferϊ-butyl-4-bromobenzylcarbamate (1.25 g, 4.37 mmol) was dissolved in DMF (12 mL). To this solution was added Ag2O (4.0 g, 17 mmol) followed by the addition of CH3I (0.68 mL, 11 mmol). The mixture was stirred at 50 0C for 18 hours. The reaction mixture was filtered through a bed of celite and the celite was washed with methanol (2 x 20 mL) and dichloromethane (2 x 20 mL). The filtrate was concentrated to remove most of the DMF. The residue was treated with water (50 mL) and a white emulsion formed. This mixture was extracted with ethyl acetate (4 x 25 mL), dried over Na2SO4, and the solvent was evaporated to yield fert-butyl-4-bromobenzyl(methyl)carbamate (1.3 g, 98%) as a yellow oil. 1H NMR (300 MHz, OMSO-d6) δ 7.53 (d, J = 8.1 Hz, 2H), 7.15 (d, J = 8.4 Hz, 2H), 4.32 (s, 2H), 2.74 (s, 3H), 1.38 (s, 9H).
[00428] Step c: tert-Butyl 4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2- yl)benzylmethylcarbamate PCTZ OSOGZ Th11eO couiSpliBng11S r1eac +ti.on was ac ,hi.eved , m . , t,he same manner as d ,escπ .,bed A a ubove f for 1 Λ- methyl-4-[4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)phenyl]sulfonyl-piperazine, Preparation AA. The Boc protecting group was removed after the coupling reaction by treating the crude reaction mixture with 0.5 mL of IN HCl in diethyl ether for 18 hours before purification by HPLC.
[00429] Additional examples of the invention were prepared following the above procedure with non-substantial changes but using aryl boronic acids given in Table 4.
[00430] Table 4: Additional exemplary compounds of formula I.
Figure imgf000143_0001
Figure imgf000144_0001
Figure imgf000145_0001
Figure imgf000146_0001
Figure imgf000147_0001
Figure imgf000148_0001
Figure imgf000149_0001
Figure imgf000150_0001
(a) The Boc protecting group was removed after the coupling reaction treating the crude reaction mixture with 0.5 mL of IN HCl in diethyl ether for 18 hours before purification by HPLC.
[00431] Further examples of the invention may be prepared by modification of intermediates as illustrated above.
Compound Derivatization After Coupling;
DD. l-(Benzordiri31dioxol-5-ylVJV-(6-(4-(2-methylpyrrolidin-l- ylsulfonyl)phenyl)pyridin-2-yl)cyclopropanecarboxamide
Figure imgf000150_0002
[00432] Step a: 4-(4,4'-Dimethoxybenzhydryl)-thiophenyl boronic acid
4,4'-Dimethoxybenzhydrol (2.7 g, 11 mmol) and 4-mercaptophenylboronic acid (1.54 g, 10 mmol) were dissolved in 20 mL AcOH and heated at 60 0C for Ih. Solvent was "evaporated and the'ϊeiϊdu'e ^as dried under high vacuum. This material was used without further purification.
[00433] Step b: 6-(4-(Bis(4-methoxyphenyl)methylthio)phenyl)pyridin-2-amine
4-(4,4'-Dimethoxybenzhydryl)-thiophenyl boronic acid (10 mmol) and 2-amino-6- bromopyridine (1.73 g, 10 mmol) were dissolved in MeCN (40 mL) followed by addition of Pd(PPh3)4 (-50 mg) and aq. K2CO3 (IM, 22 mL). The reaction mixture was heated portion wise in a microwave oven (160 °C, 400 sec). The products were distributed between ethyl acetate and water. The organic layer was washed with water, brine and dried over MgSO4. Evaporation of the volatiles yielded an oil that was used without purification in the next step. ESI-MS m/z calc. 428.0, found 429.1 (M+l).
[00434] Step c: HBenzo[d][l,3]dioxol-5-yl)-7V-(6-(4-(bis(4- methoxyphenyl)methylthio)phenyl)-pyridin-2-yl)cyclopropanecarboxamide
6-[(4,4'-Dimethoxybenzhydryl)-4-thiophenyl]pyridin-2-ylamine (-10 mmol) and 1- benzo[l,3]dioxol-5-yl-cyclopropanecarboxylic acid (2.28 g, 11 mmol) were dissolved in chloroform (25 mL) followed by the addition of TCPH (4.1 g, 12 mmol) and DIEA (5 mL, 30 mmol). The reaction mixture was heated at 65 0C for 48 h before the volatiles were removed under reduced pressure. The residue was transferred to a separatory funnel and distributed between water (200 mL) and ethyl acetate (150 mL). The organic layer was washed with 5% NaHCO3 (2 x 150 mL), water (1 x 150 mL), brine (1 x 150 mL) and dried over MgSO4. Evaporation of the solvent yielded crude l-(benzo[d][l,3]dioxol-5-yl)-iV-(6-(4-(bis(4- methoxyphenyl)-methylthio)phenyl)pyridin-2-yl)cyclopropanecarboxamide as a pale oil. ESI- MS m/z calc. 616.0, found 617.0 (M+l) (HPLC purity -85%, UV254 nm).
[00435] Step d: 4-(6-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropane- carboxamido)pyridin-2-yl)benzenesulfonic acid l-(Benzo[d][l,3]dioxol-5-yl)-N-(6-(4-(bis(4-methoxyρhenyl)methylthio)- phenyl)pyridin-2-yl)cyclopropanecarboxamide (-8.5 mmol) was dissolved in AcOH (75 mL) followed by the addition of 30% H2O2 (10 mL). Additional hydrogen peroxide (10 ml) was added 2h later. The reaction mixture was stirred at 35-45 °C overnight (-90% conversion, HPLC). The volume of reaction mixture was reduced to a third by evaporation (bath temperature below 40 0C). The reaction mixture was loaded directly onto a prep RP HPLC column (C-18) and purified. Fractions with 4-(6-(l-(benzo[d][l,3]dioxol-5- yl)cyclopropanecarboxamido)pyridin-2-yl)benzenesulfonic acid were collected and evaporated
Figure imgf000152_0001
r u i ^χ\gfl%f%^ calTbased on 4-mercaptophenylboronic acid). ESI-MS m/z calc. 438.0, found 438.9 (M+l).
[00436] Step e: 4-(6-(l-(Benzo[d][l,3]dioxol-5-yl)cycloproρane- carboxamido)pyridin-2-yl)benzene- 1-sulfonyl chloride
4-(6-(l -(Benzo[d] [ 1 ,3]dioxol-5-yl)cyclopropanecarboxarnido)pyridin-2- yl)benzenesulfonic acid (1.9 g, 4.3 mmol) was dissolved in POCl3 (30 mL) followed by the addition of SOCl2 (3 mL) and DMF (100 μl). The reaction mixture was heated at 70-80 0C for 15 min. The volatiles were evaporated and then re-evaporated with chloroform-toluene. The residual brown oil was diluted with chloroform (22 mL) and used for sulfonylation immediately. ESI-MS m/z calc. 456.0, found 457.1 (M+l).
[00437] Step f: l-(Benzo[d][l,3]dioxol-5-yl)-N-(6-(4-(2-methylpyrrolidin-l- ylsulfonyl)phenyl)pyridin-2-yl)cyclopropanecarboxamide
4-(6-(l-(Benzo[d][l,3]dioxol-5-yl)cyclopropanecarboxamido)pyridin-2-yl)benzene- 1-sulfonyl chloride (~ 35μmol, 400μl solution in chloroform) was treated with 2- methylpyrrolidine followed by the addition of DIEA (100 μl). The reaction mixture was kept at room temperature for Ih, concentrated, then diluted with DMSO (400μl). The resulting solution was subjected to HPLC purification. Fractions containing the desired material were combined and concentrated in vacuum centrifuge at 40° C to provide the trifluoroacetic salt of target material (ESI-MS m/z calc. 505.0, found 505.9 (M+l), retention time 4.06 min). 1H NMR (250 MHz, DMSO-J6) δ 1.15 (m. 2H), δ 1.22 (d, 3H, J=6.3 Hz), 6 1.41-1.47 (m, 2H), δ 1.51 (m, 2H), δ 1.52-1.59 (m, 2H), δ 3.12 (m, IH), δ 3.33 (m, IH), δ 3.64 (m, IH), δ 6.07 (s, 2H), δ 6.96-7.06 (m, 2H), δ 7.13 (d, IH, J=I.3 Hz), 6 7.78 (d, IH, J=8.2 Hz), 8 7.88 (d, 2H, J=8.5 Hz), δ 7.94 (t, IH, J=8.2 Hz), δ 8.08 (d, IH, J=8.2 Hz), δ 8.16 (d, 2H, J=8.5 Hz), δ 8.53 (s, IH).
[00438] The compounds in the following table were synthesized as described above using commercially available amines. Additional examples of the invention were prepared following the above procedure with non-substantial changes but using amines given in Table 5.
[00439] Table 5: Additional exemplary compounds of formula I.
Figure imgf000152_0002
Figure imgf000153_0001
Figure imgf000154_0003
EE. l-BenzoFl ,3]dioxol-5-yl-iV-[6-r4-r(methyl-methylsulfonyl-amino)methyll phenyll-2- pyridyll-cvclopropane-l-carboxamide (Compound No. 292)
Figure imgf000154_0001
[00440] To the starting amine (brown semisolid, 0.100 g, ~ 0.2 mmol, obtained by treatment of the corresponding t-butyloxycarbonyl derivative by treatment with IN HCl in ether) was added dichloroethane (DCE) (1.5 mL), followed by the addition of pyridine (0.063 mL, 0.78 mmol) and methansulfonyl chloride (0.03 mL, 0.4 mmol). The mixture was stirred at 65 0C for 3 hours. After this time, LC/MS analysis showed ~ 50 % conversion to the desired product. Two additional equivalents of pyridine and 1.5 equivalents of methansulfonyl chloride were added and the reaction was stirred for 2 hours. The residue was concentrated and purified by HPLC to yield l-benzo[l,3]dioxol-5-yl-N-[6-[4-[(methyl-methylsulfonyl- amino)methyl]phenyl]-2-pyridyl]-cyclopropane-l-carboxamide (0.020 g, 21% yield) as a white solid. ESI-MS m/z calc. 479.2, found 480.1 (M+l)+.
FF. (R)- 1 -(3-hydroxy-4-methoxyphenyl)-N-(6-(4-(2-(hydroxymethyl)-pyrrolidin- 1 - ylsulfonyl)phenyl)pyridin-2-yl)cvclopropanecarboxamide
Figure imgf000154_0002
[00441] (i?)-l-(3-(Benzyloxy)-4-methoxyphenyl)-iV-(6-(4-(2-
(hydroxymethyl)pyrrolidin- 1 -ylsulfonyl)phenyl)ρyridin-2-yl)cyclopropanecarboxamide (28 mg, 0.046 mmol) was dissolved in ethanol (3 mL). Palladium on charcoal (10%, 20 mg) was added and the reaction was stirred overnight under 1 atm of hydrogen. The catalyst was filtered off and the product was isolated by silica gel chromatography (50-80% EtOAc in hexane) to provide (i?)-l-(3-hydroxy-4-methoxyphenyl)-N-(6-(4-(2-(hydroxymethyl)pyrrolidin-l- ylsulfonyl)phenyl)ρyridin-2-yl)cyclopropanecarboxamide (8 mg, 34%). ESI-MS m/z calc. 523.4, found 524.3 (M+l)+. Retention time of 3.17 minutes.
[00442] 2-Amino-5-phenylpyridine (CAS [33421-40-8]) is C-I.
GG. (J?)-(l-(4-(6-Aminopyridin-2-yl)phenylsulfonyl)ρyrrolidin-2-yl) methanol hydrochloride (C-2)
TBSCI n-BuLi, B(O1Pr)3
Figure imgf000155_0001
DCM, NaHCO3
Figure imgf000155_0002
Figure imgf000155_0003
Figure imgf000155_0004
Figure imgf000155_0005
[00443] Step a: (/?)-(l-(4-Bromophenylsulfonyl)pyrrolidin-2-yl)methanol
To a mixture of sat aq. NaHCO3 (44 g, 0.53 mol), CH2Cl2 (400 mL) and ρrrolidin-2- yl-methanol (53 g, 0.53 mol) was added a solution of 4-bromo-benzenesulfonyl chloride (127 g, 0.50 mol) in CH2Cl2 (100 mL). The reaction was stirred at 20 0C overnight. The organic phase was separated and dried over Na2SO4. Evaporation of the solvent under reduced pressure provided (i?)-(l-(4-bromophenylsulfonyl)pyrrolidin-2-yl)methanol (145 g, crude), which was used in the next step without further purification. 1H NMR (CDCl3, 300 MHz) δ 7.66-7.73 (m, 4 H), 3.59-3.71 (m, 3 H), 3.43-3.51 (m, 1 H), 3.18-3.26 (m, 1 H), 1.680-1.88 (m, 3 H), 1.45-1.53 (m, 1 H). [00444] Step b: (i?)-l-(4-Bromo-benzenesulfonyl)-2-(te?t-butyl-dimethyl- silanyloxymethyl) pyrrolidine
To a solution of [l-(4-bromo-benzenesulfonyl)-pyrrolidin-2-yl] -methanol (50.0 g, 0.16 mol) and lH-imidazole (21.3 g, 0.31 mol) in CH2Cl2 (500 mL) was added tert- butylchlorodimethylsilane (35.5 g, 0.24 mol) in portions. After addition, the mixture was stirred for 1 hour at room temperature. The reaction was quenched with water (200 mL) and the separated aqueous layer was extracted with CH2Cl2 (100 mL x 3). The combined organic layers were washed with brine, dried over Na2SO4 and evaporated under vacuum to give l-(4-bromo- benzenesulfonyl)-2-(terϊ-butyldimethylsilanyloxymethyl)pyrrolidine (68.0 g, 99%). 1H NMR (300 MHz, CDCl3) δ 7.63-7.71 (m, 4 H), 3.77-3.81 (m, 1 H), 3.51-3.63 (m, 2 H), 3.37-3.43 (m, 1 H), 3.02-3.07 (m, 1 H), 1.77-1.91 (m, 2 H), 1.49-1.57 (m, 2 H), 0.87 (s, 9 H), 0.06 (d, /= 1.8 Hz, 6 H).
[00445] Step c: (i?)-4-(2-((fert-butyldimethylsilyloxy)methyl)pyrrolidin-l- ylsulfonyl) phenylboronic acid
To a solution of l-(4-bromo-benzenesulfonyl)-2-(te?t-butyl-dimethyl- silanyloxymethyl)ρyrrolidine (12.9 g, 29.7 mmol) and B(O1Pr)3 (8.4 g, 45 mmol) in dry THF (100 mL) was added dropwise /i-BuLi (2.5 M in hexane, 29.7 mL) at -70 °C. After addition, the mixture was warmed slowly to -10 0C and treated with HCl (IM, 50 mL). The organic layer was separated and the aqueous layer was extracted with ethyl acetate. The combined organic layers were dried over Na2SO4 and evaporated under vacuum. The organics were combined to give crude (i?)-4-(2-((tert-butyldimethylsilyloxy)methyl) pyrrolidin-1- ylsulfonyl)phenylboronic acid (15.0 g), which was used directly in the next step.
[00446] Step d: (6-{4-[2-(tert-Butyl-dimethyl-silanyloxymethyl)-pyrrolidine-l- sulfonyl] phenyl }pyridin-2-yl)carbamic acid tert-butyl ester
To a solution of (6-bromo-pyridin-2-yl)carbamic acid tert-butyl ester (24.6 g, 90.0 mmol) in DMF (250 mL) were added (R)-4-(2-((tørt-butyldimethylsilyloxy)-methyl) pyrrolidin- l-ylsulfonyl)phenylboronic acid (45.0 g), Pd(PPh3)4 (10.4 g, 9.0 mmol), potassium carbonate (18.6 g, 135 mol) and water (200 mL). The resulting mixture was degassed by gently bubbling argon through the solution for 5 minutes at 20 0C. The reaction mixture was then heated at 80 °C overnight. DMF was removed under vacuum. To the residue was added EtOAc (300 mL). The mixture was filtered through a pad of silica gel, which was washed with EtOAc (50 mL x 3). The combined organic extracts were evaporated under vacuum. The crude residue was purified by column (Petroleum Ether/EtO Ac 20:1) to give (6-{4-[2-(fert-butyl-dimethyl- silanyloxymethyl)pyrrolidin e-1-sulfonyl]phenyl}pyridin-2-yl)carbamic acid tert-butyl ester (22.2 g, 45% over 2-steρs). 1H NMR (300 MHz, CDCl3) δ 8.09 (d, J- 8.4 Hz, 2 H), 7.88-7.96 (m, 3 H), 8.09 (t, /= 7.8 Hz, 1 H), 7.43-7.46 (m, 1 H), 7.38 (s, 1 H), 3.83-3.88 (m, 1 H), 3.64- 3.67 (m, 1 H), 3.53-3.59 (m, 1 H), 3.41-3.47 (m, 1 H), 3.08-3.16 (m, 1 H), L82-1.91 (m, 2 H), 1.67-1.69 (m, 1 H), 1,53-1.56 (m, 10 H), 0.89 (s, 9 H), 0.08 (d, J= 2.4 Hz, 6 H).
[00447] Step e: {6-[4-(2-Hydroxymethyl-pyrrolidine-l-sulfonyl)-phenyl]pyridin-
2-yl carbamic acid tert-bnty\ ester
A solution of crude (6-{4-[2-(tert-butyl-dimethyl-silanyloxymethyl)-pyrrolidine-l- sulfonyl]phenyl}-pyridin-2-yl)carbamic acid tert-butyl ester (22.2 g, 40.5 mmol) and TBAF (21.2 g, 81.0 mmol) in DCM (300 mL) was stirred at room temperature overnight. The mixture was washed with brine (100 mL x 3), dried over Na2SO4 and evaporated under vacuum to give {6-[4-(2-hydroxymethyl-ρyrrolidine-l-sulfonyl)-phenyl]pyridin-2-yl}carbamic acid tert-butyl ester (15.0 g, 86%), which was used directly in the next step.
[00448] Step f: (R) -(1-(4-(6-Aminopyridin-2-yl)phenylsulfonyl)-pyrrolidin-2-yl) methanol hydrochloride (C-2)
A solution of {6-[4-(2-hydroxymethyl-pyrrolidine-1-sulfonyl)-phenyl]pyridin-2- yl}carbamic acid tert-butyl ester (15.0 g, 34.6 mmol) in HCl/MeOH (50 mL, 2M) was heated at reflux for 2 h. After cooling to room temperature, the reaction mixture was evaporated under vacuum and washed with EtOAc to give (R )-(1-(4-(6-aminopyridm-2- yl)phenylsulfonyl)pyrrolidin-2-yl) methanol hydrochloride (C-2; 11.0 g, 86%). 1H NMR (300 MHz, DMSCO6) δ 8.18 (d, J= 8.7 Hz, 2 H), 7.93-7.99 (m, 3 H), 7.31 (d, J = 7.2 Hz, 1 H), 7.03 (d, J= 8.7 Hz, 1 H), 3.53-3.57 (m, 2 H), 3.29-35 (m, 2 H), 3.05-3.13 (m, 1 H), 1.77-1.78 (m, 2 H), 1.40-1.45 (m, 2 H). MS (ESI) m/z (M+H)+ 334.2.
HH. Λr-(4-(6-Aminopyridin-2-yl)benzyl)methanesulfonamide (C-3)
Figure imgf000157_0001
[00449] Step a: [6-(4-Cyano-phenyl)-pyridin-2-yl]carbamic acid tert-butyl ester
A mixture of 4-cyanobenzeneboronic acid (7.35 g, 50 mmol), (6-bromo-pyridin-2- yl)carbamic acid tert-butyl ester (13.8 g, 50 mmol), Pd(Ph3P)4 (5.8 g, 0.15 mmol) and K2CO3 (10.4 g, 75 mmol) in DMF/H2O (1:1, 250 niL) was stirred under argon at 80 °C overnight. DMF was evaporated off under reduced pressure and the residue was dissolved in EtOAc (200 niL). The mixture was washed with water and brine, dried over Na2SO4, and concentrated to dryness. The residue was purified by column (Petroleum Ether/EtOAc 50:1) on silica gel to give [6-(4-cyano-phenyl)-pyridin-2-yl]carbamic acid tert-butyl ester (7.0 g, 60%). 1H NMR (300 MHz, CDCl3) δ 8.02-8.07 (m, 2 H), 7.95 (d, J- 8.4 Hz, 1 H), 7.71-7.79 (m, 3 H), 7.37- 7.44 (m, 2 H), 1.53 (s, 9 H).
[00450] Step b: [6-(4-Aminomethyl-phenyl)-pyridin-2-yl]-carbamic acid tert- butyl ester
A suspension of [6-(4-cyano-phenyl)-pyridin-2-yl]carbamic acid tert-butyl ester (7.0 g, 24 mmol), Raney Ni (1.0 g) in EtOH (500 mL) and NH3-H2O (10 mL) was hydrogenated under H2 (50 psi.) at 50 0C for 6 h. The catalyst was filtered off and the filtrate was concentrated to dryness to give [6-(4-ammomethyl~phenyl)-pyridin-2-yl]-carbamic acid tert- butyl ester, which was used directly in next step. 1H NMR (300 MHz, CDCl3) δ 7.83-7.92 (m, 3H), 7.70 (t, J = 7.8 Hz, 1 H), 7.33-7.40 (m, 4 H), 3.92 (brs, 2 H), 1.53 (s, 9 H).
[00451] Step c: {6-[4~(Methanesulfonylamino-methyl)-phenyl]-pyridin-2- yl}carbamic acid tert-butyl ester
To a solution of [6-(4-aminomethyl-phenyl)-pyridin-2-yl]-carbamic acid tert-butyl ester (5.7 g 19 mmol) and Et3N (2.88 g, 29 mmol) in dichloromethane (50 mL) was added dropwise MsCl (2.7 g, 19 mmol) at 0 0C. The reaction mixture was stirred at this temperature for 30 min, and then washed with water and brine, dried over Na2SO4 and concentrated to dryness. The residue was recrystallized with DCM/Petroleum Ether (1:3) to give {6-[4- (methanesulfonylamino-methyl)-ρhenyl]-pyridin-2-yl}carbamic acid tert-butyl ester (4.0 g, 44% over two steps). 1H NMR (300 MHz, CDCl3) δ 7.90-7.97 (m, 3 H), 7.75 (t, / = 8.4, 8.4 Hz, 1 H), 7.54-7.59 (m, 1 H), 7.38-7.44 (m, 3 H), 4.73 (br ,1 H), 4.37 (d, J = 6.0 Hz, 2 H), 2.90 (s, 3 H), 1.54 (s, 9 H).
[00452] Step d: N-(4-(6-Aminopyridin-2-yl)benzyl)methane-sulfonamide (C-3)
A mixture of {6-[4-(methanesulfonylamino-methyl)-phenyl]-pyridin-2-yl} carbamic acid tert-butyl ester (11 g, 29 mmol) in HCl/MeOH (4M, 300 mL) was stirred at room temperature overnight. The mixture was concentrated to dryness. The residue was filtered and washed with ether to give iV-(4-(6-aminopyridin-2-yl)benzyl)methane sulfonamide (C-3) (7.6 g, 80%) 1R NMR (300 MHz, DMSO-d6) δ 14.05 (br s, 1 H), 8.24 (br s, 2 H), 7.91-7.98 (m, 3 H), 7.70 (t, J = 6.0 Hz, 1 H), 7.53 (d, J = 8.1 Hz, 2 H), 7.22 (d, J = 6.9 Hz, 1 H), 6.96 (d, J = 9 Hz, 1 H), 4.23 (d, J = 5.7 Hz, 2 H), 2.89 (s, 3 H). MS (ESI) m/z (M+H)+: 278.0,
II. 4-(6-Anτinopyridin-2-yl)-N-methylbenzenesulfonamide hydrochloride (C-4)
Figure imgf000159_0001
[00453] Step a: 4-Bromo-iV-methyl-benzenesulfonamide
To a mixture of sat aq. NaHCO3 (42 g, 0.5 mol), CH2Cl2 (400 mL) and methylamine (51.7 g, 0.5 mol, 30% in methanol) was added a solution of 4-bromo-benzenesulfonyl chloride (127 g, 0.5 mol) in CH2Cl2 (100 mL). The reaction was stirred at 20 0C overnight. The organic phase was separated and dried over Na2SO4. Evaporation of the solvent under reduced pressure provided the 4-bromo-iV-methyl-benzenesulfonamide (121 g, crude), which was used in the next step without further purification. 1H NMR (CDCl3, 300 MHz) δ 7.64-7.74 (m, 4 H), 4.62-4.78 (m, 1 H), 2.65 (d, J = 5.4 Hz, 3 H).
[00454] Step b: 4-(Λr-Methylsulfamoyl)phenylboronic acid
To a solution of 4-bromo-iV-methyl-benzene sulfonamide (24.9 g, 0.1 mol) and B(O1Pr)3 (28.2 g, 0.15 mol) in THF (200 mL) was added n-BuLi (100 mL, 0.25 mol) at -70 0C. The mixture was slowly warmed to 0 0C, then 10% HCl solution was added until pH 3-4. The resulting mixture was extracted with EtOAc. The organic layer was dried over Na2SO4, and evaporated under reduced pressure to give 4-(iV-methylsulfamoyl)phenylboronic acid (22.5 g, 96%), which was used in the next step without further purification. 1H NMR (DMSO-J6, 300 MHz) δ 8.29 (s, 2 H), 7.92 (d, J = 8.1 Hz, 2 H), 7.69 (d, J = 8.4 Hz, 2 H), 2.36 (d, J = 5.1 Hz, 3 H).
[00455] Step c: ϊert-Butyl 6-(4-(iV-methylsulfamoyl)phenyl)pyridin-2-ylcarbamate To a solution of 4-(7V-methylsulfamoyl)phenylboronic acid (17.2 g, 0.08 mol) and (6- bromo-pyridin-2-yl)carbamic acid tert-butyl ester (21.9 g, 0.08 mol) in DMF (125 mL) and H2O (125 mL) were added Pd(PPh3)4 (9.2 g, 0.008 mol) and K2CO3 (16.6 g, 0.12 mol). The resulting mixture was degassed by gently bubbling argon through the solution for 5 minutes at 20 0C. The reaction mixture was then heated at 80 °C for 16 h. The mixture was evaporated under reduced pressure, then poured into H2O, and extracted with EtOAc. The organic phase was dried over Na2SO4, and was evaporated under reduced pressure to give tert-butyl 6-(4-(N- methylsulfamoyl)phenyl)pyridin-2-ylcarbamate (21 g, 58%), which was used in the next step without further purification.
[00456] Step d: 4-(6-Aminopyridin-2-yl)-iV-methylbenzenesulfonamide hydrochloride
To a solution of tert-butyl 6-(4-(7V-methylsulfamoyl)phenyl)pyridin-2-ylcarbamate (8.5 g, 23.4 mmol) in MeOH (10 mL) was added HCl/MeOH (2M, 50 mL) at room temperature. The suspension was stirred at room temperature overnight. The solid product was collected by filtration, washed with MeOH, and dried to give 4-(6-aminopyridin-2-yl)-iV- methylbenzenesulfonamide hydrochloride (5.0 g, 71%). 1H NMR (300 Hz, DMSO-4) δ 8.12 (d, J= 8.4 Hz, 2 H), 7.91-7.96 (m, 3 H), 7.58-7.66 (m, 1 H), 7.31-7.53 (m, 1 H), 7.27 (d, / = 6.6, 1 H), 6.97 (d, J = 9.0, 1 H), 2.43 (d, J = 4.8 Hz, 3 H). MS (ESI) m/z (M+H)+ 264.0.
[00457] The compounds in the following table were synthesized as described above using commercially available or previously described carboxylic acids and amines.
[00458] Table 6: Additional exemplary compounds of formula I.
Figure imgf000160_0001
Figure imgf000161_0001
[00459] Physical data for examples of the invention are given in Table 7.
[00460] Additional exemplary compounds 164-388, as shown in Table 1, can also be prepared using appropriate starting materials and methods exemplified for the previously described compounds.
[00461] Table 7: Physical data for exemplary compounds.
Figure imgf000162_0001
Figure imgf000163_0001
Figure imgf000164_0001
Figure imgf000165_0001
Figure imgf000166_0001
Figure imgf000167_0001
Figure imgf000168_0001
Figure imgf000169_0001
Figure imgf000170_0001
Figure imgf000171_0001
Figure imgf000172_0001
Figure imgf000173_0001
Figure imgf000174_0001
Figure imgf000175_0001
Figure imgf000176_0001
ASSAYS Assays for Detecting and Measuring ΔF508-CFTR Correction Properties of Compounds
JJ. Membrane potential optical methods for assaying ΔF508-CFTR modulation properties of compounds
[00462] The optical membrane potential assay utilized voltage-sensitive FRET sensors described by Gonzalez and Tsien (See, Gonzalez, J. E. and R. Y. Tsien (1995) "Voltage sensing by fluorescence resonance energy transfer in single cells" Biophys J 69(4): 1272-80, and Gonzalez, J. E. and R. Y. Tsien (1997) "Improved indicators of cell membrane potential that use fluorescence resonance energy transfer" Chem Biol 4(4): 269-77) in combination with instrumentation for measuring fluorescence changes such as the Voltage/Ion Probe Reader (VJJPR) (See, Gonzalez, J. E., K. Oades, et al. (1999) "Cell-based assays and instrumentation for screening ion-channel targets" Drug Discov Today 4(9): 431-439).
[00463] These voltage sensitive assays are based on the change in fluorescence resonant energy transfer (FRET) between the membrane-soluble, voltage-sensitive dye, DiSBAC2(3), and a fluorescent phospholipid, CC2-DMPE, which is attached to the outer leaflet of the plasma membrane and acts as a FRET donor. Changes in membrane potential (Vm) cause the negatively charged DiSBAC2(S) to redistribute across the plasma membrane and the amount of energy transfer from CC2-DMPE changes accordingly. The changes in fluorescence emission were monitored using VD?R™ JJ, which is an integrated liquid handler and fluorescent detector designed to conduct cell-based screens in 96- or 384-well microliter plates.
L Identification of Correction Compounds
[00464] To identify small molecules that correct the trafficking defect associated with DF508-CFTR; a single-addition UTS assay format was developed. The cells were incubated in serum-free medium for 16 hrs at 37 °C in the presence or absence (negative control) of test compound. As a positive control, cells plated in 384-well plates were incubated for 16 hrs at 27 °C to "temperature-correct" ΔF508-CFTR. The cells were subsequently rinsed 3X with Krebs Ringers solution and loaded with the voltage-sensitive dyes. To activate ΔF5O8- CFTR, 10 μM forskolin and the CFTR potentiator, genistein (20 μM), were added along with CF-free medium to each well. The addition of Cl'-free medium promoted Cl" efflux in response to ΔF508-CFTR activation and the resulting membrane depolarization was optically monitored using the FRET-based voltage-sensor dyes.
2. Identification of Potentiator Compounds [00465] To identify potentiators of ΔF508-CFTR, a double-addition HTS assay format was developed. During the first addition, a Cl~-free medium with or without test compound was added to each well. After 22 sec, a second addition of CF-free medium containing 2 - 10 μM forskolin was added to activate ΔF508-CFTR. The extracellular Cl" concentration following both additions was 28 mM, which promoted Cl" efflux in response to ΔF5O8-CFTR activation and the resulting membrane depolarization was optically monitored
■ using the FRET-based voltage-sensor dyes..?; SolutionsBath Solution #1: (in mM) NaCl
160, KCl 4.5, CaCl22, MgCl2 1, HEPES 10, pH 7.4 with NaOH.
Chloride-free bath solution: Chloride salts in Bath Solution #1 are substituted with gluconate salts.
CC2-DMPE: Prepared as a 10 mM stock solution in DMSO and stored at -20°C.
DiSBAC2(3): Prepared as a 10 mM stock in DMSO and stored at
-20°C.
4. Cell Culture
[00467] NIH3T3 mouse fibroblasts stably expressing ΔF508-CFTR are used for optical measurements of membrane potential. The cells are maintained at 37 0C in 5% CO2 and 90 % humidity in Dulbecco's modified Eagle's medium supplemented with 2 mM glutamine, 10 % fetal bovine serum, 1 X NEAA, β-ME, 1 X pen/strep, and 25 mM HEPES in 175 cm2 culture flasks. For all optical assays, the cells were seeded at 30,000/well in 384-well matrigel- coated plates and cultured for 2 hrs at 37 °C before culturing at 27 0C for 24 hrs for the potentiator assay. For the correction assays, the cells are cultured at 27 0C or 37 °C with and without compounds for 16 - 24 hoursElectrophysiological Assays for assaying ΔF508-CFTR modulation properties of compounds
L Using Chamber Assay
[00468] Using chamber experiments were performed on polarized epithelial cells expressing ΔF508-CFTR to further characterize the ΔF508-CFTR modulators identified in the optical assays. pRτΔF5O8-CFTR epithelial cells grown on Costar Snapwell cell culture inserts were mounted in an Ussing chamber (Physiologic Instruments, Inc., San Diego, CA), and the monolayers were continuously short-circuited using a Voltage-clamp System (Department of Bioengineering, University of Iowa, IA, and, Physiologic Instruments, Inc., San Diego, CA). Transepithelial resistance was measured by applying a 2-mV pulse. Under these conditions, the FRT epithelia demonstrated resistances of 4 KΩ/ cm2 or more. The solutions were maintained at 27 0C and bubbled with air. The electrode offset potential and fluid resistance were corrected using a cell-free insert. Under these conditions, the current reflects the flow of GT through ΔF508-CFTR expressed in the apical membrane. The Isc was digitally acquired using an MPlOOA-CE interface and AcqKnowledge software (v3.2.6; BIOPAC Systems, Santa Barbara, CA).
2. Identification of Correction Compounds
[00469] Typical protocol utilized a basolateral to apical membrane Cl" concentration gradient. To set up this gradient, normal ringer was used on the basolateral membrane, whereas apical NaCl was replaced by equimolar sodium gluconate (titrated to pH 7.4 with NaOH) to give a large Cl" concentration gradient across the epithelium. All experiments were performed with intact monolayers. To fully activate ΔF5O8-CFTR, forskolin (10 μM) and the PDE inhibitor, IBMX (100 μM), were applied followed by the addition of the CFTR potentiator, genistein (50 μM).
[00470] As observed in other cell types, incubation at low temperatures of FRT cells stably expressing ΔF508-CFTR increases the functional density of CFTR in the plasma membrane. To determine the activity of correction compounds, the cells were incubated with 10 μM of the test compound for 24 hours at 370C and were subsequently washed 3X prior to recording. The cAMP- and genistein-mediated Isc in compound-treated cells was normalized to the 270C and 37°C controls and expressed as percentage activity. Preincubation of the cells with the correction compound significantly increased the cAMP- and genistein-mediated Isc compared to the 37°C controls.
3. Identification of Potentiator Compounds
[00471] Typical protocol utilized a basolateral to apical membrane Cl" concentration gradient. To set up this gradient, normal ringers was used on the basolateral membrane and was permeabilized with nystatin (360 μg/ml), whereas apical NaCl was replaced by equimolar sodium gluconate (titrated to pH 7.4 with NaOH) to give a large Cl" concentration gradient across the epithelium. All experiments were performed 30 min after nystatin permeabilization. Forskolin (10 μM) and all test compounds were added to both sides of the cell culture inserts. The efficacy of the putative ΔF508-CFTR potentiators was compared to that of the known potentiator, genistein.
4. Solutions Basolateral solution (in mM): NaCl (135), CaCl2 (1.2), MgCl2 (1.2), K2HPO4
(2.4), KHPO4 (0.6), N-2-hydroxyethylpiρerazine- N'-2-ethanesulfonic acid (HEPES) (10), and dextrose (10). The solution was titrated to pH 7.4 with NaOH.
Apical solution (in mM): Same as basolateral solution with NaCl replaced with Na Gluconate (135).
5. Cell Culture
[00472] Fisher rat epithelial (FRT) cells expressing ΔF508-CFTR (FRT ΔF508-CFTR) were used for Ussing chamber experiments for the putative ΔF508-CFTR modulators identified from our optical assays. The cells were cultured on Costar Snapwell cell culture inserts and cultured for five days at 37 °C and 5% Cθ2in Coon's modified Ham's F-12 medium supplemented with 5% fetal calf serum, 100 U/ml penicillin, and 100 μg/ml streptomycin. Prior to use for characterizing the potentiator activity of compounds, the cells were incubated at 27 0C for 16 - 48 hrs to correct for the ΔF5O8-CFTR. To determine the activity of corrections compounds, the cells were incubated at 27 0C or 37 °C with and without the compounds for 24 hours.
6. Whole-cell recordings
[00473] The macroscopic ΔF508-CFTR current (IΛFSOS) in temperature- and test compound-corrected NIH3T3 cells stably expressing ΔF508-CFTR were monitored using the perforated-patch, whole-cell recording. Briefly, voltage-clamp recordings of IΛFSOS were performed at room temperature using an Axopatch 200B patch-clamp amplifier (Axon Instruments Inc., Foster City, CA). All recordings were acquired at a sampling frequency of 10 kHz and low-pass filtered at 1 kHz. Pipettes had a resistance of 5 - 6 MΩ when filled with the intracellular solution. Under these recording conditions, the calculated reversal potential for Cl" (EcO at room temperature was -28 mV. All recordings had a seal resistance > 20 GΩ and a series resistance < 15 MΩ. Pulse generation, data acquisition, and analysis were performed using a PC equipped with a Digidata 1320 A/D interface in conjunction with Clampex 8 (Axon Instruments Inc.). The bath contained < 250 μl of saline and was continuously perifused at a rate of 2 ml/min using a gravity-driven perfusion system.
Z Identification of Correction Compounds
[00474] To determine the activity of correction compounds for increasing the density of functional ΔF508-CFTR in the plasma membrane, we used the above-described perforated-patch-recording techniques to measure the current density following 24-hr treatment with the correction compounds. To fully activate ΔF508-CFTR, 10 μM forskolin and 20 μM genistein were added to the cells. Under our recording conditions, the current density following 24-hr incubation at 270C was higher than that observed following 24-hr incubation at 37 0C. These results are consistent with the known effects of low-temperature incubation on the density of ΔF508-CFTR in the plasma membrane. To determine the effects of correction compounds on CFTR current density, the cells were incubated with 10 μM of the test compound for 24 hours at 370C and the current density was compared to the 27°C and 37°C controls (% activity). Prior to recording, the cells were washed 3X with extracellular recording medium to remove any remaining test compound. Preincubation with 10 μM of correction compounds significantly increased the cAMP- and genistein-dependent current compared to the 37°C controls.
8. Identification of Potentiator Compounds
[00475] The ability of ΔF508-CFTR potentiators to increase the macroscopic
ΔF508-CFTR Cl" current (IΛFSOS) in NIH3T3 cells stably expressing ΔF508-CFTR was also investigated using perforated-patch-recording techniques. The potentiators identified from the optical assays evoked a dose-dependent increase in IΛFSOS with similar potency and efficacy observed in the optical assays. In all cells examined, the reversal potential before and during potentiator application was around -30 mV, which is the calculated EQ (-28 mV).
9. Solutions
Intracellular solution (in niM): Cs-asρartate (90), CsCl (50), MgCl2 (1), HEPES
(10), and 240 μg/ml amphotericin-B (pH adjusted to 7.35 with CsOH). Extracellular solution (in mM): iV-methyl-D-glucamine (NMDG)-Cl (150), MgCl2
(2), CaCl2 (2), HEPES (10) (pH adjusted to 7.35 with HCl).
10. Cell Culture
[00476] NM3T3 mouse fibroblasts stably expressing ΔF508-CFTR are used for whole-cell recordings. The cells are maintained at 37 0C in 5% CO2 and 90 % humidity in Dulbecco's modified Eagle's medium supplemented with 2 mM glutamine, 10 % fetal bovine serum, 1 X NEAA, β-ME, 1 X pen/strep, and 25 mM HEPES in 175 cm2 culture flasks. For whole-cell recordings, 2,500 - 5,000 cells were seeded on poly-L-lysine-coated glass coverslips and cultured for 24 - 48 hrs at 27 °C before use to test the activity of potentiators; and incubated with or without the correction compound at 37 °C.for measuring the activity of correctors.
11. Single-channel recordings
[00477] The single-channel actdivities of temperature-corrected ΔF508-CFTR stably expressed in NIH3T3 cells and activities of potentiator compounds were observed using excised inside-out membrane patch. Briefly, voltage-clamp recordings of single-channel activity were performed at room temperature with an Axopatch 200B patch-clamp amplifier (Axon Instruments Inc.). All recordings were acquired at a sampling frequency of 10 kHz and low-pass filtered at 400 Hz. Patch pipettes were fabricated from Corning Kovar Sealing #7052 glass (World Precision Instruments, Inc., Sarasota, FL) and had a resistance of 5 - 8 MΩ when filled with the extracellular solution. The ΔF508-CFTR was activated after excision, by adding 1 mM Mg-ATP, and 75 nM of the cAMP-dependent protein kinase, catalytic subunit (PKA; Promega Corp. Madison, WI). After channel activity stabilized, the patch was perifused using a gravity-driven microperfusion system. The inflow was placed adjacent to the patch, resulting in complete solution exchange within 1 - 2 sec. To maintain ΔF508-CFTR activity during the rapid perifusion, the nonspecific phosphatase inhibitor F" (10 mM NaF) was added to the bath solution. Under these recording conditions, channel activity remained constant throughout the duration of the patch recording (up to 60 min). Currents produced by positive charge moving from the intra- to extracellular solutions (anions moving in the opposite direction) are shown as positive currents. The pipette potential (Vp) was maintained at 80 mV.
[00478] Channel activity was analyzed from membrane patches containing < 2 active channels. The maximum number of simultaneous openings determined the number of active channels during the course of an experiment. To determine the single-channel current amplitude, the data recorded from 120 sec of ΔF5O8-CFTR activity was filtered "off-line" at 100 Hz and then used to construct all-point amplitude histograms that were fitted with multigaussian functions using Bio-Patch Analysis software (Bio-Logic Comp. France). The total microscopic current and open probability (P0) were determined from 120 sec of channel activity. The P0 was determined using the Bio-Patch software or from the relationship P0 = M(N), where I = mean current, i = single-channel current amplitude, and N = number of active channels in patch.
12. Solutions Extracellular solution (in niM): NMDG (150), aspartic acid (150), CaCl2 (5),
MgCl2 (2), and HEPES (10) (pH adjusted to 7.35 with Tris base).
Intracellular solution (in mM): NMDG-Cl (150), MgCl2 (2), EGTA (5), TES (10), and Tris base (14) (pH adjusted to 7.35 with HCl).
13. Cell Culture
[00479] NIH3T3 mouse fibroblasts stably expressing ΔF508-CFTR are used for excised-membrane patch-clamp recordings. The cells are maintained at 37 0C in 5% CO2 and 90 % humidity in Dulbecco's modified Eagle's medium supplemented with 2 mM glutamine, 10 % fetal bovine serum, 1 X NEAA, β-ME, 1 X pen/strep, and 25 mM HEPES in 175 cm2 culture flasks. For single channel recordings, 2,500 - 5,000 cells were seeded on poly-L-lysine- coated glass coverslips and cultured for 24 - 48 hrs at 27 °C before use.
[00480] The exemplified compounds of Table 1 have an activity with a range of about 100 nM and 20 μM as measured using the assays described hereinabove. The exemplified compounds of Table 1 are found to be sufficiently efficacious as measured using the assays described hereinabove.
OTHER EMBODIMENTS
[00481] It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

Claims

WHAT IS CLAIMED IS:
1. A compound of formula (I) :
Figure imgf000184_0001
(D or a pharmaceutically acceptable salt thereof, wherein:
Each R1 is an optionally substituted C1-6 aliphatic, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted C3-10 cycloaliphatic* an optionally substituted 3 to 10 membered heterocycloaliphatic, carboxy, amido, amino, halo, or hydroxy, provided that at least one R1 is an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl attached to the 5- or 6- position of the pyridyl ring;
Each R2 is hydrogen, an optionally substituted C1-6 aliphatic, an optionally substituted C3-6 cycloaliphatic, an optionally substituted phenyl, or an optionally substituted heteroaryl;
Each R3 and R3 together with the carbon atom to which they are attached form an optionally substituted C3-7 cycloaliphatic or an optionally substituted heterocycloaliphatic;
Each R4 is an optionally substituted aryl or an optionally substituted heteroaryl; and
Each n is 1, 2, 3 or 4.
2. The compound according to claim 1, wherein one Ri that is attached to 5- or 6- position of the pyridyl ring is aryl or heteroaryl, each optionally substituted with 1 , 2, or 3 of RD ; wherein RD is -Z0R9; wherein each ZD is independently a bond or an optionally substituted branched or straight Ci-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -CONRE-, -C0NRBNRE-, -CO2-, -OCO-, -NREC02-, -O- , -NREC0NRE-, -0C0NRE-, -NRENRE~, -NREC0-, -S-, -SO-, -SO2-, -NRE-, -SO2NRE-, - NRESO2-, or -NRESO2NRE-; each R9 is independently RE, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3; and each RE is independently hydrogen, an optionally substituted C1-S aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
3. The compound according to claim 2, wherein the one R1 attached to the 5- or 6- position of the pyridyl ring is phenyl optionally substituted with 1, 2, or 3 of RD.
4. The compound according to claim 3, wherein the one R1 attached to the 5- or 6- position of the pyridyl ring is a phenyl optionally substituted with 1 RD, wherein RD is -Z0Rg; each ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -O-, - NHC(O)-, -C(O)NRE-, -SO2-, -NHSO2-, -NHC(O)-, -NR5SO2-, -SO2NH-, -S02NRE-, -NH-, or - C(O)O-.
5. The compound according to claim 2, wherein one carbon unit of ZDis replaced by -0-, - NHC(O)-, -C(0)NRE-, -SO2-, -NHSO2-, -NHC(O)-, -SO-, -NR33SO2-, -SO2NH-, -SO2NRE-, - NH-, or -C(O)O-.
6. The compound according to claim 4, wherein Rg is independently an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, an optionally substituted heteroaryl, H, or halo.
7. The compound according to claim 2, wherein the one R1 attached to the 5- or 6- position of the pyridyl ring is heteroaryl optionally substituted with 1, 2, or 3 of RD.
8. The compound according to claim 7, wherein one R1 attached to the 5- or 6- position of the pyridyl ring is a 5 or 6 membered heteroaryl having 1, 2, or 3 heteroatom selected from the group consisting of oxygen, nitrogen, and sulfur, wherein the heteroaryl is substituted with 1 of RD, wherein RD is -ZDRg; each ZD is independently a bond or an optionally substituted branched or straight Ci-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -0-, -NHC(O)-, -C(O)NRE-, -SO2-, -NHSO2-, -NHC(O)-, -NRESO2-, -SO2NH-, -SO2NR1S -NH-, or -C(O)O-.
9. The compound according to claim 7, wherein one carbon unit of ZD is replaced by -O-, - NHC(O)-, -C(0)NRE-, -SO2-, -NHSO2-, -NHC(O)-, -SO-, -NRESO2-, -SO2NH-, -SO2NRE-, - NH-, or -C(O)O-.
10. The compound according to claim 8, wherein Rg is independently an optionally substituted aliphatic, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl, H, or halo.
11. The compound according to claim 1, wherein Ri that is attached to the 5- or 6- position of the pyridyl ring is:
Figure imgf000186_0001
(Z-I), or (Z-2). wherein
W1 is -C(O)-, -SO2-, or -CH2-;
D is H, hydroxyl, or an optionally substituted group selected from aliphatic, cycloaliphatic, alkoxy, and amino; and RD is defined above.
12. The compound according to claim 11 , D is OH, an optioally substituted C1-6 aliphatic, an optionally substituted C3-C8 cycloaliphatic, an optionally substituted alkoxy, or an optionally substituted amino.
13. The compound according to claim 12, D is
Figure imgf000186_0002
wherein each of A and B is independently H, an optionally substituted Cl-6 aliphatic, an optionally substituted C3-C8 cycloaliphatic, or
A and B, taken together, form an optionally substituted 3-7 membered heterocycloaliphatic ring.
14. The compound according to claim 1, wherein Ri that is attached to the 5- or 6- position of the pyridyl ring is:
Figure imgf000186_0003
^B (Z); wherein:
W1 is -C(O)-, -SO2-, or -CH2-; Each of A and B is independently H, an optionally substituted C1-6 aliphatic, an optionally substituted C3-C8 cycloaliphatic; or
A and B, taken together, form an optionally substituted 3-7 membered heterocycloaliphatic ring.
15. The compound according to claim 13, wherein A is H and B is Ci-6 aliphatic optionally substituted with 1, 2, or 3 of halo, oxo, alkyl, hydroxy, hydroxyalkyl, alkoxyalkyl, and an optionally substituted heterocycloaliphatic.
16. The compound according to claim 13, wherein A and B, taken together with the nitrogen atom to which they are attached, form an optionally substituted 3-7 membered heterocycloaliphatic ring.
17. The compound according to claim 16, wherein A and B, taken together with the nitrogen atom to which they are attached, form an optionally substituted pyrrolidinyl, piperidinyl, morpholinyl, or piperazinyl.
18. The compound according to claim 16, wherein the heterocycloaliphatic ring is optionally substituted with 1, 2, or 3 of halo, oxo, alkyl, hydroxy, hydroxyalkyl, alkoxy, alkoxyalkyl, amino, amido, or carboxy.
19. The compound according to claim 1, wherein one R1 that is attached to the 5- or 6- position of the pyridyl ring is cycloaliphatic or heterocycloaliphatic, each optionally substituted with 1, 2, or 3 of RD ; wherein RD is -Z0R^, wherein each ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -CONRE-, -CONRENRE~, -CO2-, - OCO-, -NREC02-, -0-, -NRECONRE-, -OCONRE-, -NRENRE-, -NREC0-, -S-, -SO-, -SO2-, - NRB-, -SO2NRE-, -NRESO2-, or -NRESO2NRE-; each R9 is independently RE, halo, -OH, -NH2, - NO2, -CN, -CF3, or -OCF3; and each RE is independently hydrogen, an optionally substituted C1- s aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
20. The compound according to claim 19, wherein one Ri that is attached to the 5- or 6- position of the pyridyl ring is an optionally substituted C3-C8 cycloaliphatic.
21. The compound according to claim 20, wherein one Ri that is attached to the 5- or 6- position of the pyridyl ring is an optionally substituted C3-Cs cycloalkyl or an optionally substituted C3-Cs cycloalkenyl.
22. The compound according to claim 1, wherein the one R1 attached to the 5- or 6- position of the pyridyl ring is selected from the group consisting of
Figure imgf000188_0001
Figure imgf000188_0003
Figure imgf000188_0002
Figure imgf000188_0004
Figure imgf000189_0001
Figure imgf000190_0001
Figure imgf000191_0001
Figure imgf000192_0001
23. The compound according to claim 1, wherein R2 is hydrogen.
24. The compound according to claim 1, wherein R3 and R'3 together with the carbon atom to which they are attached form an unsubstituted C3-7 cycloaliphatic or an unsubstituted heterocycloaliphatic.
25. The compound according to claim 24, wherein R3 and R'3 together with the carbon atom to which they are attached form an unsubstituted cyclopropyl, an unsubstituted cyclopentyl, or an unsubstituted cyclohexyl.
26. The compound according to claim 1, wherein R4 is an aryl or heteroaryl optionally substituted with 1, 2, or 3 of -Z0Rg, wherein each Z° is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of Z are optionally and independently replaced by -CO-, -CS-, -CONRC-, -CONRCNRC-, -CO2-, -OCO-, -NR0CO2-, -0-, -NR0CONR0-, -OCONR0-, -NR0NR0-, -NR0CO-, -S-, -SO-, -SO2-, -NR0-, - SO2NR0-, -NR0SO2-, or -NR0SO2NR0-; each R8 is independently R°, halo, -OH, -NH2, -NO2, - CN, or -OCF3; and each R is independently an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
27. The compound according to claim 26, wherein R4 is an aryl optionally substituted with 1, 2, or 3 of -Z0R8.
28. The compound according to claim 27, wherein R4 is an optionally substituted phenyl.
29. The compound according to claim 26, wherein R4 is a heteroaryl optionally substituted with 1, 2, or 3 of -Z0R8.
30. The compound according to claim 26, wherein R4 is one selected from
Figure imgf000194_0001
Figure imgf000194_0002
Figure imgf000194_0003
31. The compound according to claim 1, wherein said compound has formula (IV):
Figure imgf000194_0004
(IV) or a pharmaceutically acceptable salt thereof, wherein
RD is -Z0R9, wherein each ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -CONRE-, -C0NRENRE-, -CO2-, -OCO-, -NREC02-, -O- , -NREC0NRE-, -0C0NRE-, -NRENRE-, -NREC0-, -S-, -SO-, -SO2-, -NRE-, -S02NRE-, -NRES02-, or -NRES02NRE-;
R9 is independently RE, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3;
Each RE is independently hydrogen, an optionally substituted C1-S aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl;
R2 is C1-4 aliphatic, C3-6 cycloaliphatic, phenyl, or heteroaryl, each of which is optionally substituted, or R2 is hydrogen;
R3 and R'3 together with the carbon atom to which they are attached form a C3-7 cycloaliphatic or a C3-7 heterocycloaliphatic, each of which is optionally substituted with 1, 2, or 3 of -ZBR7, wherein each ZB is independently a bond, or an optionally substituted branched or straight C1-4 aliphatic chain wherein up to two carbon units of ZB are optionally and independently replaced by -CO-, -CS-, -CONRB-, -CONRBNRB-, -CO2-, -OCO-, -NR6CO2-, -O- , -NRBC0NRB-, -OCONRB-, -NRBNRB-, -NRBC0-, -S-, -SO-, -SO2-, -NRB-, -SO2NR8-, - NR8SO2-, or -NRBS02NRB-;
Each R7 is independently RB, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3;
Each RB is independently hydrogen, an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl;
Each R4 is an aryl or heteroaryl, each of which is optionally substituted with 1, 2, or 3 of -Z0R8, wherein each Zc is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of Zc are optionally and independently replaced by -CO-, -CS-, -CONRC-, -CONRCNRC-, -CO2-, -OCO-, -NR0CO2-, -O- , -NRcC0NRc-, -OCONR0-, -NRCNRC-, -NR0CO-, -S-, -SO-, -SO2-, -NR0-, -SO2NR0-, - NR0SO2-, or -NR0SO2NR0-;
Each R8 is independently R°, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3; and
Each R° is independently an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
32. The compound according to claim 31, wherein Z jrD i-s independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein one carbon unit of ZD is optionally replaced by -SO2-, -CONRE~, -NR5SO2-, or -SO2NRE-.
33. The compound according to claim 32, wherein ZD is an optionally substituted branched or straight C1-6 aliphatic chain wherein one carbon unit of ZD is optionally replaced by -SO2-.
34. The compound according to claim 31, wherein R9 is an optionally substituted heteroaryl or an optionally substituted heterocycloaliphatic.
35. The compound according to claim 33, wherein R9 is an optionally substituted heterocycloaliphatic having 1 or 2 nitrogen atoms and R9 attaches directly to -SO2- via one ring nitrogen.
36. The compound according to claim 1, wherein said compound has formula V-A or formula V-B:
Figure imgf000196_0001
V-A V-B or a pharmaceutically acceptable salt thereof, wherein:
T is an optionally substituted C1-2 aliphatic chain, wherein each of the carbon units is optionally and independently replaced by -CO-, -CS-, -COCO-, -SO2-, -B(OH)-, or -B(O(C1-6 alkyl))-;
Each Of R1' and R1" is an optionally substituted C1-6 aliphatic, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted 3 to 10 membered cycloaliphatic, an optionally substituted 3 to 10 membered heterocycloaliphatic, carboxy, amido, amino, halo, or hydroxy;
RD1 is attached to carbon number 3" or 4"; each RD1 and RD2 is -ZDR9, wherein each ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZD are optionally and independently replaced by -CO-, -CS-, -C0NRE-, -C0NRENRE-, -CO2-, -OCO-, -NRECO2-, -O-, -NRECONRE-, -OCONRE-, -NRERRE-, -NREC0-, -S-, -SO-, -SO2-, -NRE-, - S02NRE-, -NRES02-, or -NRES02NRE-; R9 is independently RE, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3; or Rm and RD2, taken together with atoms to which they are attached, form a 3-8 membered saturated, partially unsaturated, or aromatic ring with up to 3 ring members independently selected from the group consisting of O, NH, NRE, and S; and each RE is independently hydrogen, an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
37. The compound according to claim 36, wherein up to two methylene units of T are optionally substituted by -CO-, -CS-, -B(OH), or -B(O(C1-6 alkyl).
38. The compound according to claim 36, wherein T is an optionally substituted chain selected from the group consisting of -CH2- and -CH2CH2-.
39. The compound according to claim 36, wherein T is optionally substituted by -ZERi0; wherein each ZE is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein up to two carbon units of ZB are optionally and independently replaced by -CO-, -CS-, -C0NRF-, -CONRFNRF-, -CO2-, -OCO-, -NRFCO2-, -O-, -NRFC0NRF-, - 0C0NRF-, -NRFNRF-, -NRFCO-, -S-, -SO-, -SO2-, -NRF-, -S02NRF-, -NRFS02-, or - NRFS02NRF-; Ri0 is independently RF, halo, -OH, -NH2, -NO2, -CN, -CF3, or -OCF3; each RF is independently hydrogen, an optionally substituted C1-8 aliphatic group, an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl.
40. The compound according to claim 39, wherein T is optionally substituted by F, Cl, C1-6 alkyl, C3-8 cycloalkyl, phenyl, naphthyl, -0-(Ci-6 alkyl), -0-(C3-8 cycloalkyl), -O-phenyl, or C3-8 spiroaliphatic.
41. The compound according to claim 36, wherein T is selected from the group consisting of
-CH2-, -CH2CH2-, -CF2-, -C(CH3)2-, -C(O) μ-,
Figure imgf000197_0001
, , , , - ,C(Phenyl)2-, -
B(OH)-, and -CH(OEt)-.
42. The compound according to claim 41, wherein T is selected from the group consisting of -CH2-, -CF2-, and -C(CH3)2-.
43. The compound according to claim 36, wherein ZD is independently a bond or an optionally substituted branched or straight C1-6 aliphatic chain wherein one carbon unit of ZD is optionally replaced by -CO-, -SO-, -SO2-, -COO-, -OCO-, -C0NRE-, -NREC0-, NREC02-, -0-, -NRES02-, or -SO2NRE-.
44. The compound according to claim 36, wherein RD1 is -Z10R9, wherein R9 is halo, -OH, - NH2, -CN, -CF3, -OCF3, or an optionally substituted group selected from the group consisting of C1-6 aliphatic, C3-8 cycloaliphatic, 3-8 membered heterocycloaliphatic, C6-10 aryl, and 5-10 membered heteroaryl.
45. The compound according to claim 44, wherein R9 is F, Cl, -OH, -CN, -CF3, or -OCF3.
46. The compound according to claim 44, wherein R9 is selected from the group consisting of C1-6 straight or branched alkyl or C2-6 straight or branched alkenyl; wherein said alkyl or alkenyl is optionally substituted by 1 or 2 substituents independently selected from the group consisting of RE, oxo, halo, -OH, -NRERE, -ORE, -C00RE, and -CONRERE.
47. The compound according to claim 44, wherein R9 is C3-8 cycloaliphatic optionally substituted by 1 or 2 substituents independently selected from the group consisting of RE, oxo, halo, -OH, -NRERE, -ORE, -COORE, and -CONRERE.
48. The compound according to claim 47, wherein R9 is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or cycloheptyl.
49. The compound according to claim 44, wherein R9 is a 3-8 membered heterocyclic with 1 or 2 heteroatoms independently selected from the group consisting of O, NH, NRE, and S; wherein said heterocyclic is optionally substituted by 1 or 2 substituents independently selected from the group RE, oxo, halo, -OH, -NRERE, -0RE, -COORE, and -C0NRERE.
50. The compound according to claim 49, wherein R9 is an optionally substituted 3-8 membered heterocyclic is
Figure imgf000198_0001
51. The compound according to claim 49, wherein R9 is optionally substituted by 1 or 2 substituents independently selected from the group consisting of oxo, F, Cl, methyl, ethyl, i- propyl, ϊ-butyl, -CH2OH, -CH2CH2OH, -C(O)OH, -C(O)NH2, -CH2O(C1-6 alkyl), - CH2CH2O(C1-6 alkyl), and -C(O)(C1-6 alkyl).
52. The compound according to claim 44, wherein R9 is 5-8 membered heteroaryl with 1 or two ring atom independently selected from the group consisting of O, S, and NRE; wherein said heteroaryl is optionally substituted by 1 or 2 substituents independently selected from the group RE, oxo, halo, -OH, -NRERE, -0RE, -COORE, and -CONRERE.
53. The compound according to claim 52, wherein R9 is
Figure imgf000199_0001
54. The compound according to claim 52, wherein R >9 i •s optionally substituted by 1 or 2 substituents independently selected from the group consisting of F, Cl, methyl, ethyl, /-propyl, t- butyl, -CH2OH, -CH2CH2OH, -C(O)OH, -C(O)NH2, -CH2O(C1-6 alkyl), -CH2CH2O(Ci-6 alkyl), and -C(O)(Ci-6 alkyl).
55. The compound according to claim 36, wherein RD1 and RD2, taken together with carbons to which they are attached, form an optionally substituted 3-8 membered saturated, partially unsaturated, or aromatic ring with 0-2 ring atoms independently selected from the group consisting of O, NH, NRE, and S.
56. The compound according to claim 55, wherein RD1 and RD2, taken together with phenyl containing carbon atoms 3" and 4", is
Figure imgf000199_0002
or
57. The compound according to claim 55, wherein RD1 and RD2, taken together with phenyl containing carbon atoms 3" and 4", is optionally substituted by 1 or 2 substituents independently selected from the group consisting of RE, oxo, halo, -OH, -NRERE, -0RE, -COORE, and -
C0NRERE.
58. The compound according to claim 36, wherein RD2 is selected from the group consisting of H, C1-6 aliphatic, halo, -CN, -NH2, -CH2NH2, -OH, -0(C1-6 aliphatic), -CH2OH, -SO2(C1-6 aliphatic), -NH-SO2(C1-6 aliphatic), -C(O)O(Ci-6 aliphatic), -C(O)OH, -NHC(O)(C1-6 aliphatic), -C(O)NH2, -C(O)NH(C1-6 aliphatic), and -C(O)N(C1-6 aliphatic)2.
59. A compound of formula (I1):
Figure imgf000200_0001
(D or a pharmaceutically acceptable salt thereof, wherein: one of G1 and G2 is N and the other of G1 and G2 is CH;
Each Ri is an optionally substituted Ci-6 aliphatic, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted 3 to 10 membered cycloaliphatic, an optionally substituted 3 to 10 membered heterocycloaliphatic, carboxy, amido, amino, halo, or hydroxy, provided that at least one Ri is an optionally substituted aryl or an optionally substituted heteroaryl attached to the 5- or 6- position of the pyridyl ring;
Each R2 is hydrogen, an optionally substituted Ci-6 aliphatic, an optionally substituted
Figure imgf000200_0002
an optionally substituted phenyl, or an optionally substituted heteroaryl;
Each R3 and R3 together with the carbon atom to which they are attached form an optionally substituted C3-7 cycloaliphatic or an optionally substituted heterocycloaliphatic;
Each R4 is an optionally substituted aryl or an optionally substituted heteroaryl; and
Each n is 1, 2, 3, or 4.
60. The compound according to claim 59, wherein the compound has formula (V-A) or formula (T-B).
Figure imgf000200_0003
(T-A) (T-B) or a pharmaceutically acceptable salt thereof, wherein Ri, R2, R3, R'3, R4, and n are defined above.
61. A compound according to any one of claims 1-59, wherein the compound is selected from Table 1.
62. A pharmaceutical composition comprising:
(i) a compound according to any one of claims 1-61; and (ii) a pharmaceutically acceptable carrier.
63. The composition according to claim 62, optionally further comprising a mucolytic agent, a bronchodialator, an antibiotic, an anti-infective agent, an anti-inflammatory agent, a CFTR modulator, or a nutritional agent.
64. A method according to modulating ABC transporter activity comprising the step of contacting said ABC transporter with a compound of formula (I) or formula (I1):
Figure imgf000201_0001
I I' j wherein: one of G1 and G2 is a nitrogen, and the other is a carbon; each Ri is an optionally substituted C1-6 aliphatic, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted Cs-10 cycloaliphatic, an optionally substituted 3 to 10 membered heterocycloaliphatic, carboxy, amido, amino, halo, or hydroxy, provided that at least one R1 is an optionally substituted cycloaliphatic, an optionally substituted heterocycloaliphatic, an optionally substituted aryl, or an optionally substituted heteroaryl attached to the 5- or 6- position of the pyridyl ring; each R2 is hydrogen, an optionally substituted C1-6 aliphatic, an optionally substituted C3-6 cycloaliphatic, an optionally substituted phenyl, or an optionally substituted heteroaryl; each R3 and R'3 together with the carbon atom to which they are attached form an optionally substituted C3-7 cycloaliphatic or an optionally substituted heterocycloaliphatic; each R4 is an optionally substituted aryl or an optionally substituted heteroaryl; and each n is 1-4.
65. The method according to claim 64, wherein the ABC transporter is CFTR.
66. A method of treating or lessening the severity of a disease in a patient, wherein said disease is selected from cystic fibrosis, hereditary emphysema, hereditary hemochromatosis, coagulation-fibrinolysis deficiencies, such as protein C deficiency, Type 1 hereditary angioedema, lipid processing deficiencies, such as familial hypercholesterolemia, Type 1 chylomicronemia, abetalipoproteinemia, lysosomal storage diseases, such as I-cell disease/pseudo-Hurler, mucopolysaccharidoses, Sandhof/Tay-Sachs, Crigler-Najjar type II, polyendocrinopathy/hyperinsulemia, Diabetes mellitus, Laron dwarfism, myleoperoxidase deficiency, primary hypoparathyroidism, melanoma, glycanosis CDG type 1, congenital hyperthyroidism, osteogenesis imperfecta, hereditary hypofibrinogenemia, ACT deficiency, Diabetes insipidus (DI), neurophyseal DI, neprogenic DI, Charcot-Marie Tooth syndrome, Perlizaeus-Merzbacher disease, neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, progressive supranuclear plasy, Pick's disease, several polyglutamine neurological disorders asuch as Huntington, spinocerebullar ataxia type I, spinal and bulbar muscular atrophy, dentatorubal pallidoluysian, and myotonic dystrophy, as well as spongiform encephalopathies, such as hereditary Creutzfeldt- Jakob disease (due to prion protein processing defect), Fabry disease, Straussler-Scheinker syndrome, COPD, dry-eye disease, or Sjogren's disease, said method comprising the step of administering to said patient an effective amount of a compound of formula I or formula I1 according to any oe of claims 1-61.
67. A kit for use in measuring the activity of an ABC transporter or a fragment thereof in a biological sample in vitro or in vivo, comprising:
(i) a composition comprising a compound of formula (I) or formula (I1) according to any one of claims 1-61; and
(ii) instructions for: a) contacting the composition with the biological sample; and b) measuring activity of said ABC transporter or a fragment thereof.
68. The kit according to claim 67, further comprising instructions for a) contacting an additional composition with the biological sample; b) measuring the activity of said ABC transporter or a fragment thereof in the presence of said additional compound, and c) comparing the activity of the ABC transporter in the presence of the additional compound with the density of the ABC transporter in the presence of a composition of formula (I) or formula (I1).
69. The kit according to claim 68, wherein the kit is used to measure the density of CFTR.
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