PI-Kinase Inhibitors with Anti-Infective Activity
20220017507 · 2022-01-20
Inventors
- Jeffrey S. Glenn (Palo Alto, CA)
- Michael A. Gelman (New York, NY, US)
- Brandon Tavshanjian (San Francisco, CA, US)
- Kevan Shokat (San Francisco, CA)
- Ingrid Choong (Los Altos, CA, US)
- Mark Smith (San Francisco, CA)
Cpc classification
C07D417/12
CHEMISTRY; METALLURGY
C07D277/46
CHEMISTRY; METALLURGY
C07D277/42
CHEMISTRY; METALLURGY
International classification
C07D417/12
CHEMISTRY; METALLURGY
C07D277/42
CHEMISTRY; METALLURGY
C07D277/46
CHEMISTRY; METALLURGY
C07D417/04
CHEMISTRY; METALLURGY
Abstract
Compounds and methods are provided for the treatment of pathogen infections. In some embodiments, the anti-infective compounds have broad spectrum activity against a variety of infective diseases, where the diseases are caused by pathogens containing a basic amino acid PIP-2 pincer (BAAPP) domain that interacts with phosphatidylinositol 4,5-bisphosphate (PIP-2) to mediate pathogen replication. Also provided are methods of inhibiting a PI4-kinase and methods of inhibiting viral infection. In some embodiments, the compound is a PI4-kinase inhibiting compound that is a 5-aryl-thiazole or a 5-heteroaryl-thiazole. The subject compounds may be formulated or provided to a subject in combination with a second anti-infective agent, e.g. interferon, ribivarin, and the like.
Claims
1. A compound having the formula (XXI) ##STR00477## wherein: R.sup.2 is an alkoxy or a substituted alkoxy; R.sup.3 is hydrogen, a lower alkyl or a substituted lower alkyl; Y.sup.3 is CH or N; Z.sup.2 is absent or CO; R.sup.1 is an aryl, a substituted aryl, a heteroaryl, a substituted heteroaryl, an alkyl, a substituted alkyl, a cycloalkyl, a substituted cycloalkyl, a heterocycle or a substituted heterocycle; and R.sup.4 is selected from alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkyl-cycloalkyl, substituted alkyl-cycloalkyl, aryl, substituted aryl, heterocycle, substituted heterocycle, alkyl-heterocycle and substituted alkyl-heterocycle; or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
2. The compound of claim 1, wherein Z.sup.2 is absent.
3. (canceled)
4. The compound of claim 2, having the formula (XXXIX): ##STR00478## wherein: R.sup.41 and R.sup.43 are independently hydrogen, a lower alkyl or a substituted lower alkyl; and R.sup.42 is selected from alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkyl-cycloalkyl, substituted alkyl-cycloalkyl, heterocycle, substituted heterocycle, alkyl-heterocycle and substituted alkyl-heterocycle.
5. The compound of claim 4, having the formula (XL) or (XLI): ##STR00479## wherein: Y.sup.11 and Y.sup.12 are selected from CR″.sub.2, NR″ and O, wherein each R″ is independently H, R, an acyl or a substituted acyl; each R is independently H, an alkyl, a substituted alkyl, an alkoxy or a halogen; and n is 0, 1, 2, 3 or 4.
6. The compound of claim 5, wherein: R.sup.41 is methyl; and R.sup.42 is selected from cyclohexyl, substituted cyclohexyl, —CH.sub.2-cyclohexyl and substituted —CH.sub.2-cyclohexyl.
7. The compound of claim 4, having one of the formulae (XLIVa)-(XLIVd) and (XLVa)-(XLVd): ##STR00480## ##STR00481## wherein: R.sup.31—R.sup.35 are independently selected from hydrogen, halogen, alkyl, substituted alkyl, hydroxy, alkoxy, substituted alkoxy, acyl, substituted acyl and —CO.sub.2R, wherein R is H, alkyl or substituted alkyl.
8. The compound of claim 7, having one of the formulae (XLVIa)-(XLVId) and (XLVIIa)-(XLVIId): ##STR00482## ##STR00483## wherein: (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen and CO.sub.2R″ wherein R″ is hydrogen, alkyl or substituted alkyl; Y.sup.4 is CH, CR or O; and R.sup.41 is H, lower alkyl or substituted lower alkyl.
9. The compound of claim 1, wherein the compound is selected from the compounds of Table 2 a prodrug thereof, or a pharmaceutically acceptable salt thereof.
10. An anti-infective pharmaceutical composition comprising: the compound of claim 1; and a pharmaceutically acceptable excipient.
11. A method of inhibiting a PI4-kinase, the method comprising contacting a sample comprising the PI4-kinase with the compound of claim 1.
12. The method of claim 11, wherein the PI4-kinase is a PI4-III kinase.
13. The method of claim 12, wherein the PI4-III kinase is a PI4KIIIα- or PI4KIIIβ-kinase.
14. A method of treating a subject for an infective disease condition, the method comprising administering to the subject a pharmaceutical composition comprising an effective amount of the compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the infective disease condition is caused by infection of a pathogen susceptible to PI4-kinase inhibition.
15. The method of claim 14, wherein the infective disease condition results from infection with a virus selected from the Picornaviridae, Flaviviridae, Caliciviridae, Filoviridae, Hepeviridae and Coronavirinae families.
16. The method of claim 14, wherein the infective disease condition results from infection with a pathogen selected from HCV, rhinovirus, P. falciparum, ebola virus, Francisella tularensis, hantavirus, SARS virus, MERS virus, vaccinia, smallpox, Japanese encephalitis virus, hepatitis A virus, and influenza virus, Norovirus, PolioVirus, Enterovirus, HEV, EV71, EV68, West Nile Virus, cytomegalovirus, P. aeruginosa, and Dengue Virus.
17. The method of claim 16, wherein the pathogen is selected from EV71, EV68, human rhinoviruses, hepatitis A virus, HCV, norovirus and ebola virus.
18. The method of claim 17, wherein the compound is selected from the compounds of Tables 1 and 2.
19. The method of claim 14, wherein the compound has activity against two or more pathogens.
20. The compound of claim 8, wherein R.sup.31—R.sup.35 are independently selected from hydrogen, methyl, halogen and hydroxy, R.sup.41 is lower alkyl and Y.sup.4 is O.
21. The compound according to claim 9, wherein the compound is S-316.
Description
DETAILED DESCRIPTION OF THE EMBODIMENTS
[0076] As summarized above, compounds and methods are provided for the treatment of pathogen infections, where the compound inhibits an enzyme in the phosphatidylinositol 4,5-bisphosphate (PIP-2) synthetic pathway, including without limitation selective inhibition of PI4-kinase. In some embodiments, the anti-infective compounds have broad spectrum activity against a variety of infective diseases, where the diseases are caused by pathogens containing a basic amino acid PIP-2 pincer (BAAPP) domain that interacts with phosphatidylinositol 4,5-bisphosphate (PIP-2) to mediate replication. In certain cases, the compounds have activity against one or more viruses selected from the Picornaviridae, Flaviviridae, Caliciviridae, Filoviridae, Hepeviridae and Coronavirinae families.
[0077] In some embodiments, an anti-infective compound that is a PI4-kinase inhibiting compound is contacted with a pathogen, in a dose and for a period of time sufficient to inhibit replication. Contacting may be performed in vitro or in vivo. Such PI4-kinase inhibiting compounds may inhibit pathogen replication by inhibiting the production of PIP-2.
[0078] In some embodiments a method of inhibiting a PI4-kinase, including but not limited to a class III PI4-kinase, are provided, where a compound of the invention is brought into contact with a PI4-kinase in a dose and for a period of time sufficient to inhibit activity of the enzyme.
[0079] Also provided are pharmaceutical compositions that include the subject compounds, where a compound of the present disclosure can be formulated with a pharmaceutically acceptable excipient. Formulations may be provided in a unit dose, where the dose provides an amount of the compound effective to achieve a desired result, including without limitation inhibition of pathogen replication.
[0080] These compounds and methods find use in a variety of applications in which inhibition of a PI-kinase is desired.
Compounds
[0081] As summarized above, aspects of the disclosure include PI4-kinase inhibitor compounds. In some cases, the compounds include a 5-aryl-thiazole or a 5-heteroaryl-thiazole core structure. The 5-aryl or 5-heteroaryl ring may be a 6-membered heteroaryl (e.g., pyridyl) or phenyl ring that includes at least a further substituent meta to the thiazole ring substituent. The thiazole ring of the core structure may include further substituents at the 2- and/or 4-positions of the ring. In some embodiments, the PI4-kinase inhibitor compounds are 2-amino-5-phenylthiazole compounds that include a thiazole ring having an amino substituent at the 2-position of the ring, and a phenyl substituent at the 5-position of the ring. In some embodiments, the PI4-kinase inhibitor compounds are 2-amino-5-pyridyl-thiazole compounds that include a thiazole ring having an amino substituent at the 2-position of the ring, and a pyridyl substituent at the 5-position of the ring. In some embodiments, the compound includes further substituents, such as a substituent at either the 4 or 5-position of the thiazole ring. The aryl ring of the core structure (e.g., 5-phenyl or pyridyl ring) may be further substituted with any convenient substituents including but not limited to alkyl, acyloxy, aminoalkoxy, cyano, halogen, hydroxyl, nitro, —NHCOR, —SO.sub.2NHR, —CONHR or —NHSO.sub.2R, where R is alkyl, heteroalkyl, heterocycle or aryl. Exemplary 5-aryl-thiazole compounds are set forth in the following structures and formulae I-XLIX.
[0082] In some cases, the subject compound is described by the structure of formula (Ia):
##STR00001##
[0083] where:
[0084] Z.sup.1 and W are each independently a covalent bond or a linking functional group;
[0085] Y.sup.1 and Y.sup.2 are each independently CR.sup.2 or N;
[0086] R.sup.1 is selected from hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, an alkyl-heterocycle, a substituted heterocycle, a heterocycle and a substituted heterocycle;
[0087] R.sup.3 is selected from hydrogen and an alkyl;
[0088] R.sup.4 is selected from an alkyl, a substituted alkyl, an aralkyl, a substituted aralkyl, an aryl, a substituted aryl, an alkyl-cycloalkyl, a substituted alkyl-cyclohexyl, a cycloalkyl, a substituted cycloalkyl, an alkyl-heterocycle, a substituted alkyl-heterocycle, a heterocycle, a substituted heterocycle, an amino, a substituted amino, an alkoxy and a substituted alkoxy; and
[0089] R.sup.2, R.sup.6 and R.sup.7 are independently selected from hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, a hydroxy, an alkoxy, a substituted alkoxy, an aryloxy, a substituted aryloxy, a heterocycle, a substituted heterocycle, a cyano, a halogen, an amino, a substituted amino, an acyl, an acyloxy, an amido, and a nitro.
[0090] In some cases, the subject compound is described by the structure of formula (Ib):
##STR00002##
[0091] where:
[0092] Z.sup.1 and W are each independently a covalent bond or a linking functional group;
[0093] Y.sup.3 is CR.sup.1 or N;
[0094] R.sup.1 is selected from hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, an alkyl-heterocycle, a substituted heterocycle, a heterocycle and a substituted heterocycle;
[0095] R.sup.3 is selected from hydrogen and an alkyl;
[0096] R.sup.4 is selected from an alkyl, a substituted alkyl, an aralkyl, a substituted aralkyl, an aryl, a substituted aryl, an alkyl-cycloalkyl, a substituted alkyl-cyclohexyl, a cycloalkyl, a substituted cycloalkyl, an alkyl-heterocycle, a substituted alkyl-heterocycle, a heterocycle, a substituted heterocycle, an amino, a substituted amino, an alkoxy and a substituted alkoxy; and
[0097] R.sup.2, R.sup.6 and R.sup.7 are independently selected from hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, a hydroxy, an alkoxy, a substituted alkoxy, an aryloxy, a substituted aryloxy, a heterocycle, a substituted heterocycle, a cyano, a halogen, an amino, a substituted amino, an acyl, an acyloxy, an amido, and a nitro.
[0098] In certain embodiments, in formula (Ia) or (Ib), R.sup.1 to R.sup.7 are independently selected from corresponding groups as depicted in any of the structures of Table 1 or 2.
[0099] In some embodiments, in formula (Ia), Y′ is CH and Y.sup.2 is CR.sup.2, such that the compound is described by the formula (IIa):
##STR00003##
[0100] where:
[0101] Z.sup.1 and W are each independently a covalent bond or a linking functional group;
[0102] R.sup.1 is selected from an alkyl, an aryl, an alkyl-heterocycle and a heterocycle;
[0103] R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy;
[0104] R.sup.3 is selected from hydrogen and an alkyl;
[0105] R.sup.4 is selected from an alkyl, an aralkyl, an aryl, an alkyl-cycloalkyl, a cycloalkyl, an alkyl-heterocycle, a heterocycle; and
[0106] R.sup.6 and R.sup.7 are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen, an amino, an acyl, an acyloxy, an amido and nitro.
[0107] In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0108] In some embodiments, R.sup.3 and R.sup.6 are selected such that they form a 6-membered ring as part of a fused tricyclic aryl-thiazole core structure.
[0109] In some embodiments, R.sup.1 is not a hydroxy-substituted alkyl group, such as —(CH.sub.2).sub.2—OH.
[0110] In some embodiments, R.sup.1 is selected from hydrogen, an alkyl, an aryl (e.g., a phenyl), an alkyl-heterocycle and a heterocycle (e.g., pyridyl, pyrimidinyl, pyrrolyl, pyrrolidinyl, quinolinyl, indolyl, furyl, imidazolyl, oxazolyl, thiazolyl, 1,2,4-triazolyl, tetrazolyl, pyrrolidino, morpholino, piperazino, piperidino, tetrahydrofuranyl). In some embodiments, R.sup.1 is selected from hydrogen, a substituted lower alkyl (e.g., a substituted methyl or ethyl), a phenyl, a cycloalkyl, a pyridyl and a pyrimidinyl.
[0111] In some instances, R.sup.4 is —(CH.sub.2).sub.n—R.sup.10, where n is 0, 1, 2 or 3; and R.sup.10 is a cycloalkyl or a heterocycle (e.g., a 5- or 6-membered saturated N-containing heterocycle). In certain cases, R.sup.10 is selected from a cyclohexyl, a cyclopentyl, a cyclopropyl, a lower alkyl, a pyrrolidinyl and a piperidinyl.
[0112] In some embodiments, the subject compound is described by the structure of formula (IIb):
##STR00004##
[0113] where:
[0114] Z.sup.1 and Z.sup.2 are each independently a covalent bond or a linking functional group;
[0115] R.sup.1 is selected from hydrogen, an alkyl, a substituted alkyl (e.g., a substituted ethyl, or a heterocycle-substituted lower alkyl), an aryl (e.g., a phenyl), a substituted aryl, a heterocycle (e.g., a pyridyl, a pyrimidinyl) and a substituted heterocycle;
[0116] R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy;
[0117] R.sup.3 and R.sup.5 are selected from hydrogen and an alkyl (e.g., a lower alkyl such as a methyl);
[0118] R.sup.4 is selected from an alkyl (e.g., a cycloalkyl such as cycloheptyl, cyclohexyl, cyclopentyl, cyclopropyl or a lower alkyl such as methyl, ethyl or tert-butyl), an aralkyl (e.g., a benzyl or a phenylethyl), an aryl, an alkyl-heterocycle, a heterocycle, an amino and an alkoxy; and
[0119] R.sup.6 and R.sup.7 are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro.
[0120] In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0121] In certain embodiments, in formula (IIb), R.sup.1 to R.sup.4 are independently selected from corresponding groups as depicted in any of the structures of Table 1 or 2.
[0122] The linking functional group may be any convenient bivalent group. Linking functional groups of interest include, but are not limited to, an amino, an amido, an ester, a carbonyloxy, an ether, a carbamate, a sulfonamide, a carbonyl, a sulfonyl, a sulfinyl, or the like. In some embodiments, the linking functional group is described by one of the following formulas: —SO.sub.2NR—, —NR—, —NRC(═O)—, or —NRC(═O)NR— where each R is independently H, an alkyl, a cycloalkyl, a heterocycle, a heterocycloalkyl, an aryl or a heteroaryl; —O—; —C(═O)—; —C(═O)X— where X is NR, O or S and where R is H or an alkyl; —S(═O)— or —SO.sub.2—; where for each of the formulae depicted it is understood that both possible orientations of a functional group are included. In some embodiments, in formula (I), Z.sup.1 is —SO.sub.2NH— or —CONH— and W is a covalent bond, —NR— or —NRC(═O)—, where R is H or an alkyl. In some embodiments, in formula (II), Z.sup.1 is —NHSO.sub.2— or —SO.sub.2NH—; and Z.sup.2 is a covalent bond or —C(═O)—.
[0123] In some embodiments, R.sup.1 is described by the formula —(CH.sub.2).sub.n—CH(R.sup.8)—CHR.sup.9, where R.sup.8 is hydrogen or a lower alkyl (e.g., methyl) and R.sup.9 is hydrogen, an aryl (e.g., a phenyl) or a heterocycle (e.g., pyridyl (e.g., 3-pyridyl), pyrimidinyl, pyrrolyl, pyrrolidinyl, quinolinyl, indolyl, furyl, imidazolyl, oxazolyl, thiazolyl, 1,2,4-triazolyl, tetrazolyl, pyrrolidino, morpholino, piperazino, piperidino, tetrahydrofuranyl); and n is 0, 1, 2 or 3. In some embodiments, n is 0. In certain embodiments, R.sup.1 is a substituted ethyl group, for example, a group described by one of the following structures:
##STR00005##
[0124] In other embodiments, R.sup.1 is described by the formula:
##STR00006##
[0125] where A is a 6-membered aryl, heteroaryl, heterocyclyl, or cycloalkyl, where Z.sup.11-Z.sup.16 are independently selected from N, CR′, NR and CR′R″, where R is H or alkyl, and R′ and R″ are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro.
[0126] In some embodiments, R.sup.1 is described by the following formula:
##STR00007##
[0127] where Z.sup.13 is CR.sup.23 or N, where R.sup.22—R.sup.26 are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro.
[0128] In certain embodiments, R.sup.1 is described by the following formula:
##STR00008##
[0129] where Z.sup.13 is CR.sup.23 or N, where R.sup.23, R.sup.24 and R.sup.26 are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro.
[0130] In some embodiments, R.sup.1 is described by the following formula:
##STR00009##
[0131] where Z.sup.3 is N or CR.sup.11; Z.sup.4 is N or CR.sup.13; and R.sup.11 to R.sup.15 are each independently selected from where R.sup.22—R.sup.26 are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro. In certain embodiments, R.sup.11 to R.sup.15 are each independently selected from hydrogen, an alkyl, an alkoxy, an acyloxy, a cyano, a halogen, and hydroxyl. In certain embodiments, Z.sup.3 is CR.sup.11, Z.sup.4 is CR.sup.13; R.sup.11, R.sup.14 and R.sup.15 are each hydrogen; R.sup.12 is hydrogen, an alkoxy (e.g., methoxy) or a halogen (e.g., fluoro); and R.sup.13 is selected from hydrogen, acetyloxy, hydroxy, methoxy, cyano-methyl and halogen (e.g., fluoro). In certain embodiments, Z.sup.4 is N. In certain embodiments, Z.sup.3 and Z.sup.4 are each N.
[0132] In some instances, R.sup.1 is described by the following formula:
##STR00010##
[0133] where Z.sup.13 and Z.sup.14 are each independently CR′R″ or NR, where R is H or alkyl, and R.sup.32, R.sup.35, R.sup.36, R′ and R″ are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro. In certain embodiments, R.sup.32, R.sup.35, R.sup.36, R′ and R″ are each independently selected from hydrogen, an alkyl, an alkoxy, an acyloxy, a cyano, a halogen, and hydroxyl.
[0134] In certain embodiments, R.sup.1 is described by one of the following formulas:
##STR00011##
[0135] In some embodiments, in formulae (Ia), (Ib), (IIa) or (IIb), R.sup.2 is methoxy. In some embodiments, in formulae (Ia), (Ib), (IIa) or (IIb), R.sup.3 is methyl.
[0136] In some embodiments, in formula (IIb), Z.sup.2 is a covalent bond or —C(═O)—, and R.sup.4 is a lower alkyl (trifluoromethyl, tert-butyl, methyl, ethyl), a cycloalkyl (e.g., cyclopentyl, 1-fluoro-cyclopentyl or cyclohexyl) or —CH.sub.2-cycloalkyl, a heterocycle (e.g., a N-linked saturated heterocycle such as N-pyrollidinyl, N-morpholino), or an amino (e.g., an amino-alkyl such as N-amino-cyclopentyl). In some embodiments, in formula (IIb), R.sup.4 is described by the formula —NR.sup.16R.sup.17, wherein R.sup.16 and R.sup.17 are each independently selected from hydrogen, an alkyl, a cycloalkyl, and wherein optionally R.sup.16 and R.sup.17 are cyclically linked (e.g., to form a N-heterocyclyl). In some embodiments, in formula (IIb), Z.sup.2 is a covalent bond; and R.sup.4 is an alkyl or an alkyl-cycloalkyl (e.g., 1-cyclopentyl-methyl-). In some embodiments, in formula (IIb), R.sup.4 is selected from methyl, trifluoromethyl, ethyl, tert-butyl, cyclopentyl, N-pyrrolidinyl, N-morpholinyl, N-amino-cyclopentyl and 1-fluoro-cyclopentyl. In certain embodiments, in formula (IIb), R.sup.5 is hydrogen. In certain embodiments, in formula (II), R.sup.6 and R.sup.7 are each hydrogen.
[0137] In some instances, the compound is described by the structure of formula (III):
##STR00012##
[0138] where R.sup.1 is selected from hydrogen, an alkyl, an aryl, an alkyl-heterocycle and a heterocycle; R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.3 is alkyl; R.sup.5 is H or alkyl; R.sup.4 is lower alkyl, cycloalkyl, -alkyl-cycloalkyl, heterocyclyl or alkyl-heterocyclyl (e.g., —(CH.sub.2).sub.n-cycloalkyl or —(CH.sub.2).sub.n-heterocycyl, where n is 0, 1 or 2); W.sup.1 is —SO.sub.2— or —C(═O)—; and W.sup.2 is a covalent bond, —NH—, or —NHCO—. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0139] In certain embodiments, in formula (III), R.sup.1 is described by the following structure:
##STR00013##
[0140] where A is a 6-membered aryl, heteroaryl, heterocyclyl, or cycloalkyl, where Z.sup.11-Z.sup.16 are independently selected from N, CR′, NR and CR′R″, where R is H or alkyl, and R′ and R″ are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro.
[0141] In some embodiments, in formula (III), R.sup.1 is described by one of the following structures:
##STR00014##
[0142] where Z.sup.13 is CR.sup.23 or N, where Z.sup.3 is N or CR.sup.11; Z.sup.4 is N or CR.sup.13; and R.sup.11 to R.sup.15 and R.sup.23—R.sup.26 are each independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro.
[0143] In certain embodiments, in formula (III), R.sup.1 is described by the following:
##STR00015##
[0144] where Z.sup.13 is CR.sup.23 or N, and R.sup.23, R.sup.24 and R.sup.26 are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro. In certain embodiments, R.sup.23, R.sup.24 and R.sup.26 are independently selected from H, alkyl (e.g., methyl or ethyl), alkoxy (e.g., methoxy or ethoxy) and halo (e.g., fluoro or chloro). In certain cases, Z.sup.13 is selected from CH and N.
[0145] In certain embodiments, in formula (III), R.sup.1 to R.sup.4 are independently selected from corresponding groups as depicted in any of the structures of Table 1 or 2.
[0146] In some cases, the compound is described by the structure of formula (IV):
##STR00016##
[0147] where: R.sup.1 is —(CH.sub.2).sub.n—R.sup.20, where R.sup.20 is an aryl, a cycloalkyl or a heterocycle and n is 0, 1 or 2; R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.3 is H or alkyl; W.sup.2 is a covalent bond, —NH—, or —NHCO—; n is 0, 1, 2 or 3; and R.sup.10 is a cycloalkyl or a heterocycle. In certain cases, in formula (IV), R.sup.1 is a phenyl, a pyridyl, a diazinyl, a piperidinyl, a piperazinyl, or a pyrriloidinyl. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0148] In certain cases, in formula (IV), R.sup.1 is described by the following structure:
##STR00017##
[0149] where A is a 6-membered aryl, heteroaryl, heterocyclyl, or cycloalkyl, where Z.sup.11-Z.sup.16 are independently selected from N, CR′, NR and CR′R″, where R is H or alkyl, and R′ and R″ are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro.
[0150] In some cases, the compound is described by the structure of formula (V):
##STR00018##
[0151] where: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.3 is lower alkyl, W.sup.2 is a covalent bond, —NH—, or —NHCO—; n is 0, 1 or 2; Z.sup.13 is N or CR.sup.23, R.sup.10 is a cycloalkyl or a heterocycle; and R.sup.23—R.sup.26 are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro. In certain embodiments, R.sup.23—R.sup.26 are independently selected from hydrogen, halo, alkyl, and alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0152] In some instances, the compound is described by the structure of one of formulae (VI), (VII) or (VIII):
##STR00019##
[0153] where: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.3 is lower alkyl, n is 0, 1 or 2; Z.sup.13 is N or CR.sup.23, R.sup.16 is a cycloalkyl or a heterocycle; and R.sup.23—R.sup.26 are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro. In certain embodiments, R.sup.23—R.sup.26 are independently selected from hydrogen, halo, alkyl, and alkoxy. In certain instances, R.sup.16 is a cyclopentyl, a cyclohexyl, a piperidinyl or a pyrrolidinyl. In certain embodiments, in formulae (IV)-(VIII), R.sup.2 is methoxy. In certain embodiments, in formulae (IV)-(VIII), R.sup.3 is methyl. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0154] In certain embodiments, in formulae (IV)-(VIII), Z.sup.13, R.sup.23—R.sup.26, R.sup.2, R.sup.3 and R.sup.16 are independently selected from corresponding groups as depicted in any of the structures of Table 1 or 2.
[0155] In some cases, the compound is described by the structure of formula (IX):
##STR00020##
[0156] where: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.3 is lower alkyl; W.sup.2 is a covalent bond, —NH—, or —NHCO—; each n is independently 0, 1 or 2; Z.sup.13 is N or CR.sup.23; R.sup.16 is a cycloalkyl or a heterocycle; and R.sup.20 is an aryl, a cycloalkyl or a heterocycle. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0157] In certain cases, R.sup.20 and R.sup.10 are independently described by the following structure:
##STR00021##
[0158] where A is a 6-membered aryl, heteroaryl, heterocyclyl, or cycloalkyl, where Z.sup.11-Z.sup.16 are independently selected from N, CR′, NR and CR′R″, where R is H, an alkyl, a cycloalkyl, a heterocycloalkyl, an aryl or a heteroaryl; and R′ and R″ are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro. In certain embodiments, R.sup.20 is a phenyl, a pyridyl, a diazinyl, a piperidinyl, a piperazinyl, or a pyrrolidinyl.
[0159] In some instances, the compound is described by the structure of one of formulae (X), (XI) or (XII):
##STR00022##
[0160] where R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.3 is a lower alkyl, each n is independently 0, 1 or 2; R.sup.10 is a cycloalkyl or a heterocycle; and R.sup.20 is an aryl, a cycloalkyl or a heterocycle. In certain embodiments, R.sup.20 is a phenyl, a pyridyl, a diazinyl, a piperidinyl, a piperazinyl, or a pyrrolidinyl.
[0161] In certain instances, R.sup.10 is a cyclopentyl, a cyclohexyl, a piperidinyl or a pyrrolidinyl. In certain instances, R.sup.20 is a phenyl, or a pyridyl. In certain embodiments, in formulae (IX)-(XII), R.sup.2 is methoxy. In certain embodiments, in formulae (IX)-(XII), R.sup.3 is methyl. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0162] In some embodiments, the compound is described by the structure of formula (XIII):
##STR00023##
[0163] where R.sup.1 is an alkyl, an aryl, an alkyl-heterocycle or a heterocycle; and R.sup.4 is an alkyl, an aralkyl, an aryl, an alkyl-cycloalkyl, a cycloalkyl, an alkyl-heterocycle, or a heterocycle. In certain instances, R.sup.4 is a cyclopentyl, a cyclohexyl, a piperidinyl or a pyrrolidinyl. In certain instances, R.sup.1 is a phenyl or a pyridinyl.
[0164] In certain embodiments, in formulae (I)-(XIII), R.sup.1 or R.sup.20 is described by one of the following structures:
##STR00024##
[0165] where R.sup.44—R.sup.46 are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro; R.sup.1 is hydrogen, an alkyl, an aryl or a heterocycle; n.sup.2 is 0, 1, 2 or 3, and n.sup.1 is 0, 1 or 2; and
[0166] R.sup.4 is —(CH.sub.2).sub.n-cycloalkyl (e.g., cyclopropyl, cyclopentyl or cyclohexyl), —(CH.sub.2).sub.n-heterocycle (e.g., piperidinyl, a piperazinyl, or a pyrriloidinyl), or lower alkyl, where each n is independently 0, 1, 2 or 3. In certain embodiments, in formula (XIII), n is 1.
[0167] In certain embodiments, in formula (XIII), R.sup.1 and R.sup.4 are independently selected from corresponding groups as depicted in any of the structures of Table 1 or 2.
[0168] In certain embodiments, the compound is described by one of the following structures:
##STR00025## ##STR00026##
[0169] where R.sup.1 is selected from a phenyl, a pyridyl, a diazinyl, a piperidinyl, a piperazinyl, a pyrriloidinyl and —(CH.sub.2).sub.n—R.sup.20 where R.sup.20 is an aryl, a cycloalkyl or a heterocycle and n is 0, 1 or 2.
[0170] In certain embodiments, in the nine structures depicted above, R.sup.1 is described by one of the following structures:
##STR00027##
[0171] where R.sup.44—R.sup.46 are independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro; R.sup.1 is hydrogen, an alkyl, an aryl or a heterocycle; n.sup.2 is 0, 1, 2 or 3, and n.sup.1 is 0, 1 or 2. In certain embodiments, R.sup.44—R.sup.46 are independently selected from H, an alkyl, an alkoxy, hydroxyl, and a halo (e.g., fluoro or chloro).
[0172] In some embodiments, the compound is described by the structure of formula (XIV):
##STR00028##
[0173] where R.sup.1 is a phenyl, a pyridyl (e.g., 4-pyridyl or 3-pyridyl) or a pyrimidinyl (e.g., a 4-pyrimidinyl or 3-pyrimidinyl). In some embodiments, in formula (XIV), R.sup.5—R.sup.7 are each hydrogen. In certain embodiments, in formula (XIV), R.sup.1 to R.sup.5 are independently selected from corresponding groups as depicted in any of the structures of Table 1 or 2. In some embodiments, in formula (XIV), R.sup.1 is a phenyl, and R.sup.5—R.sup.7 are each hydrogen.
[0174] In some embodiments, the compound is described by the structure of formula (XIVb):
##STR00029##
[0175] wherein n is 0 or 1; m is 0 or 1; R.sup.2, R.sup.3, Y.sup.3 and R.sup.10 are as defined herein; R.sup.z and R.sup.z′ are cyclically linked and together form a 5- or 6-membered saturated heterocycle with the N to which they are attached (e.g., a pyrrolidinyl ring or a piperidinyl ring), where the heterocycle is optionally substituted (e.g., substituted with an amino, a hydroxy, a substituted alkoxy, an alkoxy, a substituted alkyl or an alkyl group). In certain instances, n is 1 and m is 1 and R.sup.10 is a cycloalkyl or a substituted cycloalkyl. In certain instances, n is 1 and m is 0 and R.sup.10 is a cycloalkyl or a substituted cycloalkyl. In certain instances, n is 0 and m is 0 and R.sup.10 is a cycloalkyl or a substituted cycloalkyl. In certain instances, n is 0 and m is 1 and R.sup.10 is a cycloalkyl or a substituted cycloalkyl.
[0176] In certain embodiments, the compound is described by the structure of formula (XV):
##STR00030##
[0177] where Z.sup.3 is N or CR.sup.11; Z.sup.4 is N or CR.sup.13; and R.sup.11—R.sup.15 are each independently selected from hydrogen, an alkyl (e.g., a lower alkyl such as methyl or trifluoromethyl), an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino (e.g., —NMe.sub.2), an acyl, an acyloxy, an amido, or a nitro. In some embodiments, in formula (XV), R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy (e.g., methoxy). In some embodiments, in formula (XV), R.sup.3 is an alkyl (e.g., methyl). In some embodiments, in formula (XV), Z.sup.4 is CR.sup.13 and Z.sup.3 is CR.sup.11. In some embodiments, in formula (XV), Z.sup.4 is N and Z.sup.3 is CR.sup.11. In some embodiments, in formula (XV), Z.sup.3 and Z.sup.4 are each N. In some embodiments, in formula (XV), R.sup.11—R.sup.15 are each independently selected from hydrogen, an alkoxy (e.g., methoxy), a halogen (e.g., fluoro), acyloxy (e.g., acetyloxy), hydroxy and cyano-alkyl (e.g., cyano-methyl). In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0178] In some embodiments, the subject compound is described by the structure of formula (XVI):
##STR00031##
[0179] where R.sup.17 is hydrogen, an alkoxy (e.g., methoxy) or a halogen (e.g., fluoro); and R.sup.18 is selected from hydrogen, acetyloxy, hydroxy, methoxy, cyano-methyl and halogen (e.g., fluoro), In some embodiments, in formula (XVI), R.sup.4 is selected from methyl, trifluoromethyl, ethyl, tert-butyl, cyclopentyl, N-pyrrolidinyl, N-morpholinyl, N-amino-cyclopentyl and 1-fluoro-cyclopentyl; and R.sup.17 and R.sup.18 are independently selected from hydrogen, methoxy, fluoro, acetyloxy, hydroxy, and cyano-methyl.
[0180] In some embodiments, the subject compound is described by the structure of formula (XVII):
##STR00032##
[0181] wherein: Z.sup.1 is —NHSO.sub.2— or —SO.sub.2NH—; Z.sup.2 is a covalent bond or —C(═O)—; Z.sup.3 is N or CR.sup.11; Z.sup.4 is N or CR.sup.13; and R.sup.11 to R.sup.15 are each independently selected from hydrogen, an alkyl, an aryl, a hydroxy, an alkoxy, an aryloxy, a heterocycle, a cyano, a halogen (e.g., fluoro, chloro or bromo), an amino, an acyl, an acyloxy, an amido, and a nitro. In certain embodiments, in formula (XVII), R.sup.11 to R.sup.15 are each independently selected from hydrogen, an alkoxy, an acyloxy, a halogen, and hydroxyl. In some embodiments, in formula (XVII), Z.sup.3 is CR.sup.11, Z.sup.4 is CR.sup.13; R.sup.11, R.sup.12, R.sup.14 and R.sup.15 are each hydrogen; and R.sup.13 is selected from hydrogen, acetyloxy, hydroxy, methoxy and halogen (e.g., fluoro), In some embodiments, in formula (XVII), Z.sup.3 is CR.sup.11, Z.sup.4 is N, and R.sup.11, R.sup.12, R.sup.14 and R.sup.15 are each hydrogen. In some embodiments, in formula (XVII), Z.sup.3 and Z.sup.4 are each N, and R.sup.12, R.sup.14 and R.sup.15 are each hydrogen. In some embodiments, in formula (XVII), Z.sup.2 is a covalent bond or —C(═O)—, and R.sup.4 is a lower alkyl (e.g., trifluoromethyl, tert-butyl), a cycloalkyl (e.g., cyclopentyl or 1-fluoro-cyclopentyl) or —CH.sub.2-cycloalkyl (e.g., —CH.sub.2-cyclopentyl), a heterocycle (e.g., a N-linked saturated heterocycle such as N-pyrrolidino or N-morpholino), or an amino (e.g., an amino-alkyl such as N-amino-cyclopentyl), In some embodiments, in formula (XVII), Z.sup.2 is —C(═O)—, and R.sup.4 is described by the formula —NR.sup.16R.sup.17, where R.sup.16 and R.sup.17 are each independently selected from hydrogen, an alkyl, and a cycloalkyl, wherein optionally R.sup.16 and R.sup.17 are cyclically linked (e.g., to form a N-heterocyclyl), In some embodiments, in formula (XVII), Z.sup.2 is a single bond; and R.sup.4 is an alkyl or a cycloalkyl-alkyl (e.g., 1-cyclopentyl-methyl), In some embodiments, in formula (XVII), Z.sup.2 is —C(═O)—, and R.sup.4 is selected from trifluoromethyl, ethyl, tert-butyl, N-pyrrolidinyl, N-morpholinyl, N-amino-cyclopentyl and 1-fluoro-cyclopentyl.
[0182] In some embodiments, the subject compound is described by the structure of formula (XVIII):
##STR00033##
[0183] where X and Y are independently selected from the substituents groups shown below:
##STR00034## ##STR00035##
[0184] In certain embodiments, in formula (XVIII), R.sup.1 and R.sup.4 are independently selected from corresponding groups as depicted in any of the structures of Table 1 or 2. In some embodiments, the subject compound is described by the structure of compound PT423, shown in Table 1. In some embodiments, the subject compound is described by one of the structures labeled M1, M2, and M3 in FIG. 2.
[0185] In some instances of formula (Ib), the compound has the formula (XXI):
##STR00036##
[0186] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.3 is hydrogen, a lower alkyl (e.g., methyl) or a substituted lower alkyl; Y.sup.3 is CH or N; Z.sup.2 is absent, CO or SO.sub.2; R.sup.1 is an aryl, a substituted aryl (e.g., a substituted phenyl), a heteroaryl, a substituted heteroaryl (e.g., a substituted pyridyl), an alkyl, a substituted alkyl, a cycloalkyl, a substituted cycloalkyl (e.g., a substituted cyclohexyl), a heterocycle (e.g., a tetrahydropyran or a piperidinyl) or a substituted heterocycle; and R.sup.4 is selected from alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkyl-cycloalkyl, substituted alkyl-cycloalkyl, aryl, substituted aryl, heterocycle, substituted heterocycle, alkyl-heterocycle (e.g., —CH.sub.2-(4-tetrahydropyran)) and substituted alkyl-heterocycle; or a prodrug thereof, or a pharmaceutically acceptable salt thereof. In certain instances, Z.sup.2 is absent. In certain instances, Z.sup.2 is —C(═O)—. In certain instances, Z.sup.2 is —S(═O).sub.2—. In certain instances, R.sup.1 is a phenyl, a substituted phenyl, a cyclohexyl, a substituted cyclohexyl, a piperidinyl (e.g., a 3-piperidinyl or a 4-piperidinyl) or a substituted piperidinyl (e.g., a substituted 3-piperidinyl or substituted 4-piperidinyl). In certain instances, R.sup.1 is a substituted phenyl. In certain instances, R.sup.1 is a substituted alkyl, e.g., a substituted lower alkyl. In certain instances, R.sup.4 is a cyclohexyl, a substituted cyclohexyl, a tetrahydropyran, a benzyl, a substituted benzyl, a phenyl, a substituted phenyl, a methylene-cyclohexane and a substituted methylene-cyclohexane. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0187] In certain embodiments of formula (XXI), the compound has formula (XXII):
##STR00037##
[0188] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.10 is selected from cycloalkyl, substituted cycloalkyl, heterocycle (e.g., 4-tetrahydropyran) and substituted heterocycle; and R.sup.51 and R.sup.52 are independently selected from H, halogen (e.g., fluoro), alkyl (e.g., lower alkyl) and substituted alkyl. In certain instances, R.sup.1 is a phenyl, a substituted phenyl, a cyclohexyl, a substituted cyclohexyl, a piperidinyl (e.g., a 3-piperidinyl or a 4-piperidinyl) or a substituted piperidinyl (e.g., a substituted 3-piperidinyl or substituted 4-piperidinyl). In certain instances, R.sup.1 is a substituted phenyl. In certain instances, R.sup.1 is a substituted alkyl, e.g., a substituted lower alkyl. In certain instances, R.sup.10 is a cyclohexyl, a substituted cyclohexyl, a tetrahydropyran, a benzyl, a substituted benzyl, a phenyl, a substituted phenyl, a methylene-cyclohexane and a substituted methylene-cyclohexane. In certain instances, R.sup.51 and R.sup.52 are each hydrogen. In certain instances, R.sup.51 is hydrogen and R.sup.52 is alkyl or substituted alkyl (e.g., methyl). In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0189] In certain embodiments of formula (XXII), the compound has formula (XXIII):
##STR00038##
[0190] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.31—R.sup.35 are independently selected from hydrogen, halogen (e.g., fluoro), alkyl, substituted alkyl, hydroxy, alkoxy, substituted alkoxy, acyl, substituted acyl and —CO.sub.2R, wherein R is H, alkyl or substituted alkyl. In certain instances, R.sup.31 and R.sup.33 are halogen (e.g., fluoro or chloro). In certain instances, R.sup.31 and R.sup.35 are halogen (e.g., fluoro or chloro). In certain instances, R.sup.31 is halogen (e.g., fluoro or chloro). In certain instances, 3 or 4 of R.sup.31-R.sup.35 are hydrogen. In certain instances, R.sup.51 and R.sup.52 are each hydrogen. In certain instances, R.sup.51 is hydrogen and R.sup.52 is alkyl or substituted alkyl (e.g., methyl). In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0191] In certain embodiments of formulae (XXII) or (XXIII), the compound has the formula (XXIV) or formula (XXV):
##STR00039##
[0192] wherein: one and only one of R.sup.33 and R.sup.34 is hydroxy; and R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy. In certain instances, R.sup.33 is hydroxy. In certain instances, R.sup.34 is hydroxy. In certain instances, 3, 4 or 5 of R.sup.31-R.sup.35 are hydrogen. In certain cases, R.sup.10 is a cyclohexyl or substituted cyclohexyl. In certain cases, R.sup.10 is tetrahydropyran (e.g., 4-tetrahydropyranyl) or substituted tetrahydropyran (e.g., substituted 4-tetrahydropyranyl). In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0193] In certain embodiments of formula (XXIV) and formula (XXV), the compound has one of the formulae (XXVI)-(XXVIII):
##STR00040##
[0194] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.31, R.sup.32, R.sup.34 and R.sup.35 are independently selected from hydrogen and halogen (e.g., fluoro); and (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro), and CO.sub.2R″ where R″ is hydrogen, alkyl or substituted alkyl. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe. In certain embodiments, the compound has one of the following structures:
##STR00041##
[0195] or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
[0196] In certain embodiments of formula (XXIII), the compound has formula (XXIX):
##STR00042##
[0197] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.31—R.sup.35 are independently selected from hydrogen and halogen (e.g., fluoro or chloro), wherein 0, 1 or 2 of R.sup.31—R.sup.35 are halogen; and (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro) and CO.sub.2R″ wherein R″ is hydrogen, alkyl or substituted alkyl. In certain instances, R.sup.31 and R.sup.33 are halogen (e.g., fluoro or chloro). In certain instances, R.sup.31 and R.sup.35 are halogen (e.g., fluoro or chloro). In certain instances, R.sup.31 is halogen (e.g., fluoro or chloro). In certain instances, 3 or 4 of R.sup.31-R.sup.35 are hydrogen. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0198] In certain embodiments of formula (XXII), the compound has formula (XXX):
##STR00043##
[0199] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.4 is a lower alkyl or a substituted lower alkyl (e.g., an isopropyl); and (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro), and CO.sub.2R″ where R″ is hydrogen, alkyl or substituted alkyl. In certain instances, n is 0. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0200] In certain embodiments of formula (XXII), the compound has the formula (XXXI):
##STR00044##
[0201] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; each (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro) and CO.sub.2R″ where R″ is hydrogen, alkyl or substituted alkyl. In certain instances, each n is 0. In certain instances, each n is 0. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0202] In certain embodiments, the compound has the structure:
##STR00045##
[0203] or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
[0204] In certain embodiments of formula (XXIII), the compound has the formula (XXXII):
##STR00046##
[0205] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.31—R.sup.33 and R.sup.35 are independently selected from hydrogen and halogen (e.g., fluoro); (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro) and CO.sub.2R″ where R″ is hydrogen, alkyl or substituted alkyl; and R′ is H, alkyl or substituted alkyl. In certain embodiments, R′ is a lower alkyl. In certain cases, R′ is ethyl. In certain cases, R′ is methyl. In certain embodiments, n is 0. In certain embodiments, R.sup.31—R.sup.33 and R.sup.35 are each hydrogen. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe. In certain embodiments, the compound has the structure:
##STR00047##
wherein R′ is H, a lower alkyl or a substituted lower alkyl; or a prodrug thereof, or a pharmaceutically acceptable salt thereof. In certain cases, R′ is hydrogen. In certain cases, R′ is lower alkyl. In certain cases, R′ is ethyl. In certain cases, R′ is methyl.
[0206] In some embodiments, the compound has the following structure:
##STR00048##
[0207] where R.sup.31—R.sup.35 are selected from one of the following embodiments:
TABLE-US-00001 Embodiment R.sup.31 R.sup.32 R.sup.33 R.sup.34 R.sup.35 1 H H H H H 2 F H F H H 3 Cl H H H H 4 Cl H Cl H H 5 Cl H H H Cl
[0208] In certain embodiments of formula (XXI), the compound has the formula (XXXIII) or formula (XXXIV):
##STR00049##
wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.3 is hydrogen, a lower alkyl (e.g., methyl) or a substituted lower alkyl; R.sup.1 is an aryl, a substituted aryl, (e.g., a substituted phenyl), a heteroaryl, a substituted heteroaryl, (e.g., a substituted pyridyl), a cycloalkyl, a substituted cycloalkyl (e.g., a substituted cyclohexyl), a heterocycle (e.g., a tetrahydropyran or a piperidinyl) or a substituted heterocycle; and R.sup.4 is selected from alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkyl-cycloalkyl, substituted alkyl-cycloalkyl, heterocycle, substituted heterocycle, alkyl-heterocycle (e.g., —CH.sub.2-(4-tetrahydropyran)) and substituted alkyl-heterocycle. In certain instances, R.sup.1 is a phenyl, a substituted phenyl, a cyclohexyl, a substituted cyclohexyl, a piperidinyl (e.g., a 3-piperidinyl or a 4-piperidinyl) or a substituted piperidinyl (e.g., a substituted 3-piperidinyl or substituted 4-piperidinyl). In certain instances, R.sup.1 is a substituted phenyl. In certain instances, R.sup.4 is a cyclohexyl, a substituted cyclohexyl, a tetrahydropyran, a methylene-tetrahydropyran, a substituted tetrahydropyran, a substituted methylene-tetrahydropyran, a benzyl, a substituted benzyl, a phenyl, a substituted phenyl, a methylene-cyclohexane and a substituted methylene-cyclohexane. In certain instances, R.sup.4 is cycloheptyl or a substituted cycloheptyl. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe.
[0209] In certain embodiments of formulae (XXXIII) or (XXXIV), the compound has one of the formula (XXXV) and formula (XXXVI):
##STR00050##
[0210] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro), and CO.sub.2R″ where R″ is hydrogen, alkyl and substituted alkyl. In certain instances, n is 0. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe. In certain embodiments, R.sup.1 is phenyl or substituted phenyl (e.g., as described in any of the compounds of Tables 1-2). In certain embodiments, R.sup.1 is pyridyl (e.g., 2-pyridyl, 3-pyridyl or 4-pyridyl) or substituted pyridyl (e.g., as described in compounds of Tables 1-2). In certain embodiments, R.sup.1 is a saturated heterocycle or a substituted saturated heterocycle.
[0211] In some embodiments of formula (XXXV) and formula (XXXVI), the compound has one of the formula (XXXVII) and formula (XXXVIII):
##STR00051##
[0212] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.31—R.sup.35 are independently selected from hydrogen, halogen (e.g., fluoro), alkyl, substituted alkyl, hydroxy, alkoxy, substituted alkoxy, acyl, substituted acyl and —CO.sub.2R, wherein R is H, alkyl or substituted alkyl. In certain embodiments of formula (XXXVII) and formula (XXXVIII), R.sup.31—R.sup.35 are independently selected from hydrogen, methyl, halogen (e.g., fluoro or chloro) and hydroxy. In certain instances, R.sup.31 and R.sup.33 are halogen (e.g., fluoro or chloro). In certain instances, R.sup.31 and R.sup.35 are halogen (e.g., fluoro or chloro). In certain instances, R.sup.31 is halogen (e.g., fluoro or chloro). In certain instances, 3 or 4 of R.sup.31-R.sup.35 are hydrogen. In certain embodiments of formula (XXXVII) and formula (XXXVIII), R.sup.31 and R.sup.35 are independently lower alkyl or substituted lower alkyl (e.g., methyl). In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe. In certain instances, the compound has the structure:
##STR00052##
or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
[0213] In some embodiments, the compound has one of the following structures:
##STR00053##
[0214] where R.sup.31—R.sup.35 are selected from one of the following embodiments:
TABLE-US-00002 Embodiment R.sup.31 R.sup.32 R.sup.33 R.sup.34 R.sup.35 1 Cl H H H Cl 2 Cl H H H F 3 Cl H Cl H H 4 Cl H H H H 5 Me H OH H H 6 Cl H OH H H
[0215] In some embodiments of formula (XXI), the compound has the formula (XXXIX):
##STR00054##
[0216] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; R.sup.41 and R.sup.43 are independently hydrogen, a lower alkyl or a substituted lower alkyl (e.g., methyl); and R.sup.42 is selected from alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkyl-cycloalkyl, substituted alkyl-cycloalkyl, heterocycle, substituted heterocycle, alkyl-heterocycle (e.g., —CH.sub.2-(4-tetrahydropyran)) and substituted alkyl-heterocycle. In certain cases, Y.sup.3 is N. In certain cases, Y.sup.3 is CH. In certain embodiments, R.sup.1 is phenyl or substituted phenyl (e.g., as described in any of the compounds of Tables 1-2). In certain embodiments, R.sup.1 is pyridyl (e.g., 2-pyridyl, 3-pyridyl or 4-pyridyl) or substituted pyridyl (e.g., as described in compounds of Tables 1-2). In certain embodiments, R.sup.1 is a saturated heterocycle or a substituted saturated heterocycle. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe. In certain embodiments, R.sup.43 is H. In certain embodiments, R.sup.41 is alkyl or substituted alkyl. In certain embodiments, R.sup.41 and R.sup.43 are independently alkyl or substituted alkyl. In certain embodiments of formula (XXXIX), the compound has the formula (XL) or (XLI):
##STR00055##
[0217] wherein: R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl, an alkoxy and a substituted alkoxy; Y.sup.11 and Y.sup.12 are selected from CR″.sub.2, NR″ and O, wherein each R″ is independently H, R, an acyl or a substituted acyl; each R is independently H, an alkyl, a substituted alkyl, an alkoxy or a halogen (e.g., a fluoro); and n is 0, 1, 2, 3 or 4. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe. In certain embodiments, Y.sup.11 is CH(OH). In certain embodiments, Y.sup.11 is CH(OR), where R is acyl (e.g., acetyl) or substituted acyl. In certain embodiments, Y.sup.11 is O. In certain embodiments, Y.sup.11 is NH.
[0218] In certain embodiments of formula (XL) or (XLI), the compound has the formulae (XLII) or (XLIII):
##STR00056##
In some instances, Y.sup.11 and Y.sup.12 are each NH. In certain cases, n is 0 (e.g., there are no R groups present). In some instances of formulae (XL)-(XLIII), (R).sub.n is 4-CO.sub.2R′, wherein R′ is hydrogen or lower alkyl (e.g., ethyl). In certain embodiments of formulae (XXXIX)-(XLIII), R.sup.41 is methyl; and R.sup.42 is selected from cyclohexyl, substituted cyclohexyl, —CH.sub.2-cyclohexyl and substituted —CH.sub.2-cyclohexyl. In certain embodiments, Y.sup.11 is CH(OH). In certain embodiments, Y.sup.11 is CH(OR), where R is acyl (e.g., acetyl) or substituted acyl. In certain embodiments, Y.sup.11 is O. In certain embodiments, Y.sup.11 is NH. In certain embodiments, the compound has one of the following structures:
##STR00057##
or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
In certain embodiments of formula (XXXIX), the compound has one of the formulae (XLIVa)-(XLIVh) and (XLVa)-(XLVh):
##STR00058## ##STR00059## ##STR00060## ##STR00061##
wherein: R.sup.31—R.sup.35 are independently selected from hydrogen, halogen (e.g., fluoro), alkyl, substituted alkyl, hydroxy, alkoxy, substituted alkoxy, acyl, substituted acyl and —CO.sub.2R, wherein R is H, alkyl or substituted alkyl, R.sup.41 is H, alkyl or substituted alkyl, and R.sup.43 is alkyl or substituted alkyl. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe. In certain embodiments, R.sup.41 and R.sup.43 are each independently alkyl or substituted alkyl. In certain embodiments, R.sup.41 and R.sup.43 are each methyl. In certain embodiments, R.sup.42 is alkyl or substituted alkyl. In certain embodiments, R.sup.42 is methyl, ethyl, isopropyl, propyl. In certain embodiments, R.sup.41 and R.sup.43 are each methyl and R.sup.42 is a lower alkyl or substituted lower alkyl (e.g., methyl, ethyl, isopropyl, propyl). In certain embodiments, R.sup.42 is a saturated heterocycle (e.g., 4-tetrahydropyran) or substituted saturated heterocycle. In certain embodiments, R.sup.42 is a cycloalkyl or substituted cycloalkyl. In certain embodiments of formula (XLIVa-d), R.sup.41 is alkyl or substituted alkyl and R.sup.42 is a saturated heterocycle (e.g., 4-tetrahydropyran) or substituted saturated heterocycle. In certain embodiments of formula (XLIVe-h), R.sup.41—R.sup.43 are independently alkyl or substituted alkyl. In certain embodiments of formula (XLIVe-h), R.sup.41 and R.sup.43 are each lower alkyl and R.sup.42 is alkyl or substituted alkyl. In certain embodiments of formula (XLVa-d), R.sup.41 is alkyl or substituted alkyl and R.sup.42 is a saturated heterocycle (e.g., 4-tetrahydropyran) or substituted saturated heterocycle. In certain embodiments of formula (XLVe-h), R.sup.41—R.sup.43 are independently alkyl or substituted alkyl. In certain embodiments of formula (XLVe-h), R.sup.41 and R.sup.43 are each lower alkyl and R.sup.42 is alkyl or substituted alkyl.
[0219] In certain embodiments of formulae (XLIVa-h) and formulae (XLVa-h), the compound has one of the formulae (XLVIa)-(XLVId) and (XLVIIa)-(XLVIId):
##STR00062## ##STR00063##
[0220] wherein: (R).sub.n is one or more optional substituents (i.e., n is 0, 1, 2, 3, 4 or 5) each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro) and CO.sub.2R″ where R″ is hydrogen, alkyl or substituted alkyl; Y.sup.4 is CH, CR or O; and R.sup.41 is H, lower alkyl or substituted lower alkyl. In certain instances of formula (XLVIa-d) and formula (XLVIIa-d), R.sup.31—R.sup.35 are independently selected from hydrogen, methyl, halogen (e.g., fluoro or chloro) and hydroxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.31—R.sup.35 are selected as described in one of the compounds of Tables 1-2. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe. In certain embodiments, Y.sup.4 is CH. In certain embodiments, Y.sup.4 is CR, wherein R is not H. In certain embodiments, Y.sup.4 is O. In certain embodiments, R.sup.41 is lower alkyl or substituted lower alkyl. In certain embodiments, R.sup.41 is H. In certain instances, R.sup.31—R.sup.35 are independently selected from hydrogen, methyl, halogen and hydroxy, R.sup.41 is lower alkyl (e.g., methyl) and Y.sup.4 is O.
[0221] In some embodiments, the compound has the following structure:
##STR00064##
[0222] where R and R.sup.31—R.sup.35 are selected from one of the following embodiments:
TABLE-US-00003 Embodiment R R.sup.31 R.sup.32 R.sup.33 R.sup.34 R.sup.35 1 CO.sub.2Et H H OH H H 2 CO.sub.2Et H H H H H 3 CO.sub.2Et F H F H H 4 CO.sub.2Et Cl H H H H 5 CO.sub.2Et Cl H Cl H H 6 CO.sub.2Et Cl H H H Cl 7 H H H OH H H 8 H H H H H H 9 H F H F H H 10 H Cl H H H H 11 H Cl H Cl H H 12 H Cl H H H Cl
[0223] In some embodiments, the compound has the following structure:
##STR00065##
where R.sup.31—R.sup.35 are selected from one of the following embodiments:
TABLE-US-00004 Embodiment R.sup.31 R.sup.32 R.sup.33 R.sup.34 R.sup.35 1 H H OH H H 2 H H H H H 3 F H F H H 4 Cl H H H H 5 Cl H Cl H H 6 Cl H H H Cl
[0224] In certain instances of formula (XXI), the compound has one of the formula (XLVIII) or formula (XLIX):
##STR00066##
[0225] wherein R.sup.1 is selected from aryl, substituted aryl, heteroaryl and substituted heteroaryl. In certain instances of formula (XLVIII) or formula (XLIX): R.sup.4 is methyl, isopropyl, cyclohexyl, substituted cyclohexyl, phenyl, substituted phenyl, benzyl, substituted benzyl or —CH.sub.2-4-tetrahydropyran. In certain instances of formula (XLVIII) or formula (XLIX): R.sup.1 is a substituted phenyl (e.g., 4-hydroxy-phenyl). In certain embodiments, R.sup.2 is selected from hydrogen, a halogen and an alkoxy. In certain embodiments, R.sup.2 is selected from hydrogen, a halogen, an alkyl, a substituted alkyl and an alkoxy. In certain embodiments, R.sup.2 is selected from a lower alkyl, a halogen, a substituted lower alkyl, and a lower alkoxy. In certain embodiments, R.sup.2 is selected from Me, Cl, Br, CHF.sub.2, CF.sub.3, CH.sub.2F and OMe. Also provided are compounds based on any of the structure and formulae depicted herein having OMe at the R.sup.2 position, which have an analogous structure but with one Me, Cl, Br, CHF.sub.2, CF.sub.3 and CH.sub.2F appearing at the R.sup.2 position instead of this OMe group.
[0226] In some embodiments, the compound has the following structure:
##STR00067##
[0227] where Y.sup.3 and R.sup.4 are selected from one of the following embodiments:
TABLE-US-00005 Embodiment Y.sup.3 R.sup.4 1 CH methyl 2 CH isopropyl 3 CH cyclohexyl 4 CH phenyl 5 CH benzyl 6 CH —CH.sub.2—(4-tetrahydropyran) 7 N methyl 8 N isopropyl 9 N cyclohexyl 10 N phenyl 11 N benzyl 12 N —CH.sub.2—(4-tetrahydropyran)
[0228] In some embodiments of any one of the formulae (Ia)-(XLIX), R.sup.2 is methoxy. In some embodiments of any one of the formulae (Ia)-(XLIX), R.sup.3 is methyl. In some embodiments of any one of the formulae (Ia)-(XLIX), R.sup.2 is methoxy and R.sup.3 is methyl. In some embodiments of any one of the formulae (Ia)-(XLIX), R.sup.2 is a halogen (e.g., Cl or Br). In some embodiments of any one of the formulae (Ia)-(XLIX), R.sup.2 is a substituted lower alkyl. In some embodiments of any one of the formulae (Ia)-(XLIX), R.sup.2 is CF.sub.3. In some embodiments of any one of the formulae (Ia)-(XLIX), R.sup.2 is CHF.sub.2. In some embodiments of any one of the formulae (Ia)-(XLIX), R.sup.2 is CH.sub.2F. In some embodiments of any one of the formulae (Ia)-(XLIX), R.sup.2 is a lower alkyl. In some embodiments of any one of the formulae (Ia)-(XLIX), R.sup.2 is methyl.
[0229] In certain embodiments, the compound is described by the structure of one of the compounds of Table 1 or Table 2. It is understood that any of the compounds shown in Table 1 or 2 may be present in a salt form, such as a trifluoroacetate salt (e.g., CF.sub.3COOH salt). In some cases, the salt form of the compound is a pharmaceutically acceptable salt.
TABLE-US-00006 TABLE 1 Compounds Cmpd Structure S-1
TABLE-US-00007 TABLE 2 Compounds Compounds Cmpd # Structure S-315
[0230] In certain embodiments, the compound is described by the structure of one of the compounds of Table 1. In certain embodiments, the compound is described by the structure of one of the compounds of Table 2. It is understood that any of the compounds shown in Table 1 or 2 may be present in a salt form, such as a trifluoroacetate salt (e.g., CF.sub.3COOH salt). In some cases, the salt form of the compound is a pharmaceutically acceptable salt.
[0231] Aspects of the present disclosure include PI-kinase inhibiting compounds, salts thereof (e.g., pharmaceutically acceptable salts), and/or solvate, hydrate and/or prodrug forms thereof. In addition, it is understood that, in any compound described herein having one or more chiral centers, if an absolute stereochemistry is not expressly indicated, then each center may independently be of R-configuration or S-configuration or a mixture thereof. It will be appreciated that all permutations of salts, solvates, hydrates, prodrugs and stereoisomers are meant to be encompassed by the present disclosure.
[0232] In some embodiments, the subject compounds, or a prodrug form thereof, are provided in the form of pharmaceutically acceptable salts. Compounds containing an amine or nitrogen containing heteraryl group may be basic in nature and accordingly may react with any number of inorganic and organic acids to form pharmaceutically acceptable acid addition salts. Acids commonly employed to form such salts include inorganic acids such as hydrochloric, hydrobromic, hydriodic, sulfuric and phosphoric acid, as well as organic acids such as para-toluenesulfonic, methanesulfonic, oxalic, para-bromophenylsulfonic, carbonic, succinic, citric, benzoic and acetic acid, and related inorganic and organic acids. Such pharmaceutically acceptable salts thus include sulfate, pyrosulfate, bisulfate, sulfite, bisulfate, phosphate, monohydrogenphosphate, dihydrogenphosphate, metaphosphate, pyrophosphate, chloride, bromide, iodide, acetate, propionate, decanoate, caprylate, acrylate, formate, isobutyrate, caprate, heptanoate, propiolate, oxalate, malonate, succinate, suberate, sebacate, fumarate, maleate, butyne-1,4-dioate, hexyne-1,6-dioate, benzoate, chlorobenzoate, methylbenzoate, dinitrobenzoate, hydroxybenzoate, methoxybenzoate, phthalate, terephathalate, sulfonate, xylenesulfonate, phenylacetate, phenylpropionate, phenylbutyrate, citrate, lactate, β-hydroxybutyrate, glycollate, maleate, tartrate, methanesulfonate, propanesulfonates, naphthalene-1-sulfonate, naphthalene-2-sulfonate, mandelate, hippurate, gluconate, lactobionate, and the like salts. In certain specific embodiments, pharmaceutically acceptable acid addition salts include those formed with mineral acids such as hydrochloric acid and hydrobromic acid, and those formed with organic acids such as fumaric acid and maleic acid.
[0233] In some embodiments, the subject compounds are provided in a prodrug form. “Prodrug” refers to a derivative of an active agent that requires a transformation within the body to release the active agent. In certain embodiments, the transformation is an enzymatic transformation. Prodrugs are frequently, although not necessarily, pharmacologically inactive until converted to the active agent. “Promoiety” refers to a form of protecting group that, when used to mask a functional group within an active agent, converts the active agent into a prodrug. In some cases, the promoiety will be attached to the drug via bond(s) that are cleaved by enzymatic or non enzymatic means in vivo. Any convenient prodrug forms of the subject compounds can be prepared, e.g., according to the strategies and methods described by Rautio et al. (“Prodrugs: design and clinical applications”, Nature Reviews Drug Discovery 7, 255-270 (February 2008)). In some cases, the promoiety is attached to a hydroxy or carboxylic acid group of the subject compounds. In certain cases, the promoiety is an acyl or substituted acyl group. In certain cases, the promoiety is an alkyl or substituted alkyl group, e.g., that forms an ester functional group when attached to a carboxylic acid group of the subject compounds.
[0234] In some embodiments, the subject compounds, prodrugs, stereoisomers or salts thereof are provided in the form of a solvate (e.g., a hydrate). The term “solvate” as used herein refers to a complex or aggregate formed by one or more molecules of a solute, e.g. a prodrug or a pharmaceutically-acceptable salt thereof, and one or more molecules of a solvent. Such solvates are typically crystalline solids having a substantially fixed molar ratio of solute and solvent. Representative solvents include by way of example, water, methanol, ethanol, isopropanol, acetic acid, and the like. When the solvent is water, the solvate formed is a hydrate.
[0235] In some embodiments, the subject compounds are provided by oral dosing and absorbed into the bloodstream. In some embodiments, the oral bioavailability of the subject compounds is 30% or more. Modifications may be made to the subject compounds or their formulations using any convenient methods to increase absorption across the gut lumen or their bioavailability.
[0236] In some embodiments, the subject compounds are metabolically stable (e.g., remain substantially intact in vivo during the half-life of the compound). In certain embodiments, the compounds have a half-life (e.g., an in vivo half-life) of 5 minutes or more, such as 10 minutes or more, 12 minutes or more, 15 minutes or more, 20 minutes or more, 30 minutes or more, 60 minutes or more, 2 hours or more, 6 hours or more, 12 hours or more, 24 hours or more, or even more.
PI-Kinase Inhibition
[0237] As summarized above, aspects of the invention include PI4-kinase inhibiting compounds, and methods of inhibition using the same. The PI4-kinase inhibiting compounds are compounds that inhibit the activity of a PI4-kinase in a cell, upon contact with a cell or components thereof. In some instances, the types of cells in which the compounds of the invention exhibit activity are ones that have been infected with a pathogen, as described herein. By inhibiting a PI-kinase it is meant that the activity of the enzyme is decreased by a factor of 2 or more, such as 3 or more, 5 or more, 10 or more, 100 or more, or 1000 or more, relative to its normal activity (e.g., relative to a positive control).
[0238] In some embodiments, the subject compounds are inhibitors of a PI3-kinase. In some embodiments, the subject compounds are inhibitors of a PI4-kinase, such as a PI4-III-kinase (e.g., PI4-IIIα or PI4-IIIβ). In some embodiments, the subject compounds have a PI-kinase inhibition profile that reflects activity against two or more PI-kinases. In some embodiments, the subject compounds specifically inhibit both a type II PI3-kinase, such as PI3-kinase IIβ, and a type III PI4-kinase, such as PI4K-IIIα and/or PI4K-IIIβ). In some embodiments, the subject compounds specifically inhibit a PI4-kinase without undesired inhibition of protein kinases. In some embodiments, the subject compounds specifically inhibit a PI4-kinase without undesired inhibition of PI3-kinase. In some embodiments, the subject compounds specifically inhibit a PI4-kinase and/or a specific PI3-kinase subclass without undesired inhibition of other PI3-kinase subclasses or protein kinases.
[0239] In some embodiments, the compounds of the disclosure interfere with the interaction of a BAAPP domain with PIP2 in a pathogen (e.g., HCV). For example, the subject compounds may act by decreasing the levels of PIP2 either directly or indirectly that bind specifically to the BAAPP domain of the pathogen. In general, pathogens that include a BAAPP domain are susceptible to inhibition by the subject compounds.
[0240] In some embodiments, the subject compounds inhibit a PI4-kinase, as determined by an inhibition assay, e.g., by an assay that determines the level of activity of the enzyme either in a cell-free system or in a cell after treatment with a subject compound, relative to a control, by measuring the IC.sub.50 or EC.sub.50 value, respectively. In certain embodiments, the subject compounds have an IC.sub.50 value (or EC.sub.50 value) of 10 μM or less, such as 3 μM or less, 1 μM or less, 500 nM or less, 300 nM or less, 200 nM or less, 100 nM or less, 50 nM or less, 30 nM or less, 10 nM or less, 5 nM or less, 3 nM or less, 1 nM or less, or even lower.
[0241] In some embodiments, the subject compounds inhibit a PI4-kinase, as determined by a kinase activity assay, e.g., by an assay that determines the level of incorporation of radiolabeled phosphate from [γ-.sup.32P]-ATP into a substrate molecule after treatment with a subject compound, relative to a control, by measuring the beta-particle emission rate using a scintillation counter or phosphorimaging. In certain embodiments, the subject compounds have an IC.sub.50 value for PI4K-IIIβ of less than about 1 μM, less than about 0.2 μM, less than about 0.1 μM, less than about 10 nM, less than about 1 nM, or even less, such as described in Tables 2-3. In certain embodiments, the subject compounds have an IC.sub.50 value for PI4K-IIIα of less than about 50 μM, less than about 10 μM, less than about 1 μM, less than about 0.1 μM, less than about 10 nM, less than about 1 nM, or even less, such as described in Tables 2-3. In certain further embodiments, the subject compounds have an IC50 value for PI4K-IIIβ of 50 μM or less, [etc., etc.], 10 nM or less, 6 nM or less, or even less, such as described in Tables 2-3. In certain further embodiments, the subject compounds have an IC50 value for the PI3-kinase p110a-p85 complex of between about 8 and about 10 nM, between about 8 μM and about 10 μM, or even more. In certain further embodiments, the subject compounds have an IC50 value for the PI3-kinase p110γ-p85 complex of from about 2 to about 4 nM, of from about 4 μM to 5 μM, or even more, such as described herein. In certain further embodiments, the subject compounds have an IC50 value for the type II PI3-kinase beta of less than about 1 μM, less than about 150 nM, less than about 30 nM, or even less, such as described herein. In certain embodiments, the subject compounds have an IC50 value for type II PI3-kinase alpha of less than 10 μM. In certain further embodiments, more than one of the above criteria is independently satisfied by a particular compound.
[0242] In some embodiments, the potency of the PI4-kinase inhibiting compounds track with anti-infective (e.g., antiviral) activity. In some cases, the enzymatic and anti-infective activities of the subject compounds diverge. In some embodiments, the anti-infective activity of the subject compounds depends on a combination of inhibition of both PI4KIIIα and PI4KIIIβ, or a combination of inhibition of class III PI4-kinases and class II PI3-kinases (especially class II PI3-kinase beta). The subject compound may have increased specificity for one isoform of these PI-kinase family members.
[0243] In certain embodiments, the subject compounds have no significant effect on the viability of a mammalian cell, as determined by a cell cytotoxicity assay, e.g., as determined by administering a subject compound to a HeLa cell and determining the number of viable cells present. The subject compounds may exhibit a % cell viability, as compared to a control (e.g., a DMSO control), of 15% or more, such as 20% or more, 30% or more, 40% or more, 50% or more, 60% or more, 70% or more, 80% or more, 90% or more, 100% or more, 120% or more, or even higher. The subject compounds may exhibit a CC.sub.50 value of 1 nM or higher, such as 100 nM or higher, 300 nM or higher, 1 μM or higher, 3 μM or higher, 5 μM or higher, 10 μM or higher, 20 μM or higher, 30 μM or higher, 50 μM or higher, or even higher.
[0244] In certain embodiments, the compounds have a therapeutic index (e.g., the ratio of a compound's cytotoxicity (e.g., cell cytotoxicity, CC50) to bioactivity (e.g., antiviral activity, EC50)) that is 20 or more, such as 50 or more, 100 or more, 200 or more, 300 or more, 400 or more, 500 or more, or even more.
[0245] As summarized above, aspects of the disclosure include methods of inhibiting a PI-kinase (e.g., a PI3, a PI4-IIIα, or a PI4-IIIβ kinase). A subject compound (e.g., as described herein) may inhibit at least one activity of the PI-kinase in the range of 10% to 100%, e.g., by 10% or more, 20% or more, 30% or more, 40% or more, 50% or more, 60% or more, 70% or more, 80% or more, or 90% or more. In certain assays, a subject compound may inhibit its target with an IC50 of 1×10.sup.−6 M or less (e.g., 1×10.sup.−6 M or less, 1×10.sup.−7 M or less, 1×10.sup.−8 M or less, 1×10.sup.−9 M or less, 1×10.sup.−10 M or less, or 1×10.sup.−11 M or less).
[0246] The protocols that may be employed in determining PI-kinase activity are numerous, and include but are not limited to cell-free assays, e.g., binding assays; assays using purified enzymes, cellular assays in which a cellular phenotype is measured, e.g., gene expression assays; and in vivo assays that involve a particular animal (which, in certain embodiments may be an animal model for a condition related to the target pathogen).
[0247] In some embodiments, the subject method is an in vitro method that includes contacting a sample with a subject compound that specifically inhibits a target PI-kinase. In certain embodiments, the sample is suspected of containing the PI-kinase and the subject method further comprises evaluating whether the compound inhibits the PI-kinase. In certain embodiments, the PI-kinase is a PI4-kinase or a PI-3 kinase.
[0248] In certain embodiments, the subject compound is a modified compound that includes a label, e.g., a fluorescent label, and the subject method further includes detecting the label, if present, in the sample, e.g., using optical detection.
[0249] In certain embodiments, the compound is modified with a support or with affinity groups that bind to a support (e.g. biotin), such that any sample that does not bind to the compound may be removed (e.g., by washing). The specifically bound target PI-kinase, if present, may then be detected using any convenient means, such as, using the binding of a labeled target specific probe, or using a fluorescent protein reactive reagent.
[0250] In another embodiment of the subject method, the sample is known to contain the target PI-kinase.
Methods
[0251] Contrary to the classic paradigm of anti-infective therapy, the present disclosure provides methods of treating pathogen infection by targeting a host function and/or molecule upon which the pathogen is dependent, thereby decreasing the ability of the pathogen to avoid the therapeutic agent by mutation. In addition, by utilizing such a target, the methods of the disclosure allow combination therapies in which multiple targets are addressed, thereby increasing the ability to eliminate the infectious agent. The methods also provide a broad platform for anti-infective therapies by targeting a host function. In addition, in cases where the pathogen encodes its own PI-kinase(s), the present disclosure provides methods of treating pathogen infection by targeting the pathogen PI-kinase.
[0252] Pathogens of interest include those described in Glenn et al., “PIP-2 Inhibition-Based Antiviral and Anti-Hyperlipidemic Therapies” WO2009/148541, the disclosure of which is herein incorporated by reference in its entirety. Pathogens of interest include, but are not limited to, pathogens of the viral families Picornaviridae, Flaviviridae, Filoviridae, Caliciviridae, Coronavirinae, Hepeviridae, Bunyaviridae, Poxviridae and Orthomyxoviridae. In some embodiments, the pathogen is selected from hepacivirus (e.g., HCV), norovirus, hepevirus (e.g., HEV), betacoronvirus (e.g., SARS or MERS), rhinovirus (e.g., B or C), P. falciparum, Ebola virus, Francisella tularensis, hantavirus, vaccinia, smallpox, Japanese encephalitis virus, hepatitis A virus, and influenza virus, PolioVirus, Enterovirus (e.g., A-D), EV71, EV68, human rhinovirus, human poliovirus, hepatovirus (e.g., HAV), West Nile Virus, and Dengue Virus (e.g., 1-4).
[0253] In some embodiments, where the pathogen is HCV, useful compounds include those having a high first-pass effect and consequent low systemic bioavailability, which are targeted to the liver, and which are typically discarded in early drug development. In other embodiments for the treatment of HCV, the compound, or formulation, is modified for liver-specific targeting.
[0254] In some cases, the method is a method of inhibiting a PI4-kinase in a sample.
[0255] As such, aspects of the method include contacting a sample with a subject compound (e.g., as described above) under conditions by which the compound inhibits the PI4-kinase. Any convenient protocol for contacting the compound with the sample may be employed. The particular protocol that is employed may vary, e.g., depending on whether the sample is in vitro or in vivo. For in vitro protocols, contact of the sample with the compound may be achieved using any convenient protocol. In some instances, the sample includes cells that are maintained in a suitable culture medium, and the complex is introduced into the culture medium. For in vivo protocols, any convenient administration protocol may be employed. Depending upon the potency of the compound, the cells of interest, the manner of administration, the number of cells present, various protocols may be employed.
[0256] The term “sample” as used herein relates to a material or mixture of materials, typically, although not necessarily, in fluid form, containing one or more components of interest.
[0257] In some embodiments, the subject method is a method of treating a subject for an infective disease. In some embodiments, the subject method includes administering to the subject an effective amount of a subject compound (e.g., as described herein) or a pharmaceutically acceptable salt thereof. The subject compound may be administered as part of a pharmaceutical composition (e.g., as described herein). In certain instances of the method, the compound that is administered is a compound of one of formulae (Ia)-(XLIX). In certain instances of the method, the compound that is administered is described by one of the compounds of Table 1 or 2.
[0258] In some embodiments, an “effective amount” is an amount of a subject compound that, when administered to an individual in one or more doses, in monotherapy or in combination therapy, is effective to reduce viral load in the individual by at least about 20% (20% suppression), at least about 30% (30% suppression), at least about 40% (40% suppression), at least about 50% (50% suppression), at least about 60% (60% suppression), at least about 70% (70% suppression), at least about 80% (80% suppression), or at least about 90% (90% suppression), compared to the load in the individual in the absence of treatment with the compound, or alternatively, compared to the bacterial load in the individual before or after treatment with the compound.
[0259] In some embodiments, an “effective amount” of a compound is an amount that, when administered in one or more doses to an individual having a viral infection, is effective to achieve a 1.5-log, a 2-log, a 2.5-log, a 3-log, a 3.5-log, a 4-log, a 4.5-log, or a 5-log reduction in virus in the serum of the individual.
[0260] In some embodiments, an effective amount of a compound is an amount that ranges from about 50 ng/ml to about 50 μg/ml (e.g., from about 50 ng/ml to about 40 μg/ml, from about 30 ng/ml to about 20 μg/ml, from about 50 ng/ml to about 10 μg/ml, from about 50 ng/ml to about 1 μg/ml, from about 50 ng/ml to about 800 ng/ml, from about 50 ng/ml to about 700 ng/ml, from about 50 ng/ml to about 600 ng/ml, from about 50 ng/ml to about 500 ng/ml, from about 50 ng/ml to about 400 ng/ml, from about 60 ng/ml to about 400 ng/ml, from about 70 ng/ml to about 300 ng/ml, from about 60 ng/ml to about 100 ng/ml, from about 65 ng/ml to about 85 ng/ml, from about 70 ng/ml to about 90 ng/ml, from about 200 ng/ml to about 900 ng/ml, from about 200 ng/ml to about 800 ng/ml, from about 200 ng/ml to about 700 ng/ml, from about 200 ng/ml to about 600 ng/ml, from about 200 ng/ml to about 500 ng/ml, from about 200 ng/ml to about 400 ng/ml, or from about 200 ng/ml to about 300 ng/ml).
[0261] In some embodiments, an effective amount of a compound is an amount that ranges from about 10 pg to about 100 mg, e.g., from about 10 pg to about 50 pg, from about 50 pg to about 150 pg, from about 150 pg to about 250 pg, from about 250 pg to about 500 pg, from about 500 pg to about 750 pg, from about 750 pg to about 1 ng, from about 1 ng to about 10 ng, from about 10 ng to about 50 ng, from about 50 ng to about 150 ng, from about 150 ng to about 250 ng, from about 250 ng to about 500 ng, from about 500 ng to about 750 ng, from about 750 ng to about 1 μg, from about 1 μg to about 10 μg, from about 10 μg to about 50 μg, from about 50 μg to about 150 μg, from about 150 μg to about 250 Kg, from about 250 μg to about 500 μg, from about 500 μg to about 750 μg, from about 750 μg to about 1 mg, from about 1 mg to about 50 mg, from about 1 mg to about 100 mg, or from about 50 mg to about 100 mg. The amount can be a single dose amount or can be a total daily amount. The total daily amount can range from 10 pg to 100 mg, or can range from 100 mg to about 500 mg, or can range from 500 mg to about 1000 mg.
[0262] In some embodiments, a single dose of a compound is administered. In other embodiments, multiple doses are administered. Where multiple doses are administered over a period of time, the compound can be administered twice daily (qid), daily (qd), every other day (qod), every third day, three times per week (tiw), or twice per week (biw) over a period of time. For example, a compound is administered qid, qd, qod, tiw, or biw over a period of from one day to about 2 years or more. For example, a compound is administered at any of the aforementioned frequencies for one week, two weeks, one month, two months, six months, one year, or two years, or more, depending on various factors.
[0263] Administration of an effective amount of a subject compound to an individual in need thereof can result in one or more of: 1) a reduction in viral load; 2) a reduction in viral load in a target biological sample; 3) a reduction in the spread of a virus from one cell to another cell in an individual; 4) a reduction in viral entry into (e.g., reduction of internalization of a virus into) a cell; 5) a reduction in time to seroconversion; 6) an increase in the rate of sustained response to therapy; 7) a reduction of morbidity or mortality in clinical outcomes; 8) shortening the total length of treatment when combined with other anti-viral agents; and 9) an improvement in an indicator of disease response (e.g., a reduction in one or more symptoms of a viral infection, such as fever, etc.). Any of a variety of methods can be used to determine whether a treatment method is effective. For example, a biological sample obtained from an individual who has been treated with a subject method can be assayed.
[0264] In some embodiments of the methods of treatment, the infective disease condition results from infection with a positive-stranded RNA virus, negative stranded RNA virus, or a DNA virus. In some embodiments, the infective disease condition results from infection with a pathogen selected from the group of viral families consisting of Picornaviridae, Flaviviridae, Filoviridae, Caliciviridae,
[0265] Coronavirinae, Hepeviridae, Bunyaviridae, Poxviridae, and Orthomyxoviridae. In some embodiments, the infective disease condition results from infection with a pathogen selected from the phylum Apicomplexa or from the order Kinetoplastida. In some embodiments, the infective disease condition results from infection with a bacterium. In some embodiments, the infective disease condition results from infection with a pathogen selected from HCV, rhinovirus (e.g., A, B or C, as well as unclassified), P. falciparum, Ebola virus, Francisella tularensis, hantavirus, SARS virus, MERS virus, vaccinia, smallpox, Japanese encephalitis virus, hepatitis A virus, and influenza virus, Norovirus, PolioVirus, Enterovirus (e.g., A-D), HEV, EV71, EV68, West Nile Virus, and Dengue Virus (e.g., 1-4). In some embodiments, the pathogen is HCV. In some embodiments, the pathogen is rhinovirus or P. falciparum. In some embodiments, the pathogen is hepatitis A virus. In certain embodiments of the method of treatment, the pathogen is a virus selected from EV71, EV68, human rhinoviruses, HAV, HCV, norovirus and ebola virus. In some embodiments, the pathogen is hepatitis A virus. In certain cases, the virus is EV71 or EV68. In certain cases, the virus is a human rhinovirus. In certain cases, the virus is HAV. In certain cases, the virus is a norovirus. In certain cases, the virus is ebola virus. Any of the compounds described herein can be utilized in the subject methods of treatment. In certain instances, the compound is of one of formulae I-XLIX. In certain cases, the compound is one of the compounds of Table 1 or 2. In some cases, the compound that is utilized in the subject methods has broad spectrum activity against several of the pathogens (e.g., viruses) described herein. In certain instances, the compound has anti-viral activity against particular viruses, including one or more of the viruses described above.
[0266] In some embodiments, the pathogen is characterized by having a BAAPP domain that interacts with PIP-2, or a protein that binds PI(4,5)P.sub.2 or PI(4)P. In some embodiments, the pathogen is characterized by having a protein that interacts with one or more PI-4 kinases or PI phosphatases. In some embodiments, the BAAPP domain is derived from NS5A or NS4B protein. In some embodiments, the infective disease condition is caused by infection of a pathogen susceptible to PI4-kinase inhibition. In some embodiments, the compound specifically inhibits the PI4-kinase. In some embodiments, the compound has broad spectrum activity against two or more pathogens. In some embodiments, the compound modulates the activity of PIP-2. In some embodiments, the compound interferes with the interaction of a BAAPP domain and PIP-2 of the pathogen. In some embodiments, the compound blocks pathogen replication.
[0267] In some embodiments, the subject method is a method of treating a subject for an elevated level of VLDL or LDL cholesterol. In some embodiments, the subject method includes administering to the subject an effective amount of a 2-aminophenylthiazole compound (e.g., as described above), alone or in combination with other drugs known to affect LDL or VLDL levels (e.g., 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors such as lovastatin, fluvastatin, atorvastatin, pravastatin, simvastatin, rosuvastatin, etc.; microsomal triglyceride transfer protein inhibitors such as lomitapide; inhibitors of intestinal cholesterol absorption such as ezetimibe; peroxisome proliferator-activated receptor type alpha activators such as fenofibrate).
[0268] In some embodiments, the subject is human. The subject may be in need of treatment for a viral infection, or may be at risk of a viral infection. In some instances, the subject methods include diagnosing a viral infection, including any one of the viruses described herein. In some embodiments, the compound is administered as a pharmaceutical preparation.
[0269] In some embodiments, the subject method is a method of inhibiting viral infection, the method including contacting virus-infected cells with an effective dose of a 2-aminophenylthiazole compound (e.g., as described above) to inhibit viral replication. In some embodiments, the method further includes contacting the cells with a second antiviral agent.
[0270] In some embodiments, the compound is formulated to be targeted to the liver.
[0271] In certain embodiments, the compound is a modified compound that includes a label, and the method further includes detecting the label in the subject. The selection of the label depends on the means of detection. Any convenient labeling and detection systems may be used in the subject methods, see e.g., Baker, “The whole picture,” Nature, 463, 2010, p977-980. In certain embodiments, the compound includes a fluorescent label suitable for optical detection. In certain embodiments, the compound includes a radiolabel for detection using positron emission tomography (PET) or single photon emission computed tomography (SPECT). In some cases, the compound includes a paramagnetic label suitable for tomographic detection. The subject compound may be labeled, as described above, although in some methods, the compound is unlabeled and a secondary labeling agent is used for imaging.
Utility
[0272] The compounds and methods of the invention, e.g., as described herein, find use in a variety of applications. Applications of interest include, but are not limited to: research applications and therapeutic applications. Methods of the invention find use in a variety of different applications including any convenient application where inhibition of a PI4-kinase is desired.
[0273] The subject compounds and methods find use in a variety of research applications. The subject compounds and methods may be used in the optimization of the bioavailability and metabolic stability of compounds.
[0274] The subject compounds and methods find use in a variety of therapeutic applications. Therapeutic applications of interest include those applications in which pathogen infection is the cause or a compounding factor in disease progression. As such, the subject compounds find use in the treatment of a variety of different conditions in which the inhibition and/or treatment of viral infection in the host is desired. For example, the subject compounds and methods may find use in treating a pathogen caused infective disease (e.g., as described herein), such as HCV.
[0275] In some embodiments, the subject compound and methods find use in therapeutic applications in which an enterovirus infection is implicated. Enteroviruses (EVs) are among the most frequent infectious agents in humans worldwide and represent the leading cause of upper respiratory tract infections. EV infection with pulmonary exacerbations is implicated in cystic fibrosis (CF) patients. In certain instances, the subject methods and compounds (e.g., as described herein) find use in treating a cystic fibrosis (CF) patient, e.g., to reduce a symptom or condition associated with EV infection. In certain instances, the subject compounds and methods can be used to target the F508del-cystic fibrosis transmembrane conductance regulator (CFTR) folding defect.
Pharmaceutical Compositions
[0276] The herein-discussed compounds can be formulated using any convenient excipients, reagents and methods. Compositions are provided in formulation with a pharmaceutically acceptable excipient(s). A wide variety of pharmaceutically acceptable excipients are known in the art and need not be discussed in detail herein. Pharmaceutically acceptable excipients have been amply described in a variety of publications, including, for example, A. Gennaro (2000) “Remington: The Science and Practice of Pharmacy,” 20th edition, Lippincott, Williams, & Wilkins; Pharmaceutical Dosage Forms and Drug Delivery Systems (1999) H. C. Ansel et al., eds., 7.sup.th ed., Lippincott, Williams, & Wilkins; and Handbook of Pharmaceutical Excipients (2000) A. H. Kibbe et al., eds., 3.sup.rd ed. Amer. Pharmaceutical Assoc.
[0277] The pharmaceutically acceptable excipients, such as vehicles, adjuvants, carriers or diluents, are readily available to the public. Moreover, pharmaceutically acceptable auxiliary substances, such as pH adjusting and buffering agents, tonicity adjusting agents, stabilizers, wetting agents and the like, are readily available to the public.
[0278] In some embodiments, the subject compound is formulated in an aqueous buffer. Suitable aqueous buffers include, but are not limited to, acetate, succinate, citrate, and phosphate buffers varying in strengths from 5 mM to 100 mM. In some embodiments, the aqueous buffer includes reagents that provide for an isotonic solution. Such reagents include, but are not limited to, sodium chloride; and sugars e.g., mannitol, dextrose, sucrose, and the like. In some embodiments, the aqueous buffer further includes a non-ionic surfactant such as polysorbate 20 or 80. Optionally the formulations may further include a preservative. Suitable preservatives include, but are not limited to, a benzyl alcohol, phenol, chlorobutanol, benzalkonium chloride, and the like. In many cases, the formulation is stored at about 4° C. Formulations may also be lyophilized, in which case they generally include cryoprotectants such as sucrose, trehalose, lactose, maltose, mannitol, and the like. Lyophilized formulations can be stored over extended periods of time, even at ambient temperatures. In some embodiments, the subject compound is formulated for sustained release.
[0279] In some embodiments, the subject compound and an antiviral agent, e.g. interferon, ribavirin, Enfuvirtide; RFI-641 (4,4″-bis-{4,6-bis-[3-(bis-carbamoylmethyl-sulfamoyl)-phenylamino]-(1,3,5) triazin-2-ylamino}-biphenyl-2,2″-disulfonic acid); BMS-433771 (2H-Imidazo(4,5-c)pyridin-2-one, 1-cyclopropyl-1,3-dihydro-3-((1-(3-hydroxypropyl)-1H-benzimidazol-2-yl)methyl)); arildone; Pleconaril (3-(3,5-Dimethyl-4-(3-(3-methyl-5-isoxazolyflpropoxy)phenyl)-5-(trifluoromethyl)-1,2,4-oxadiazole); Amantadine (tricyclo[3.3.1.1.3,7]decane-1-amine hydrochloride); Rimantadine (alpha-methyltricyclo[3.3.1.1.3,7]decane-1-methanamine hydrochloride); Acyclovir (acycloguanosine); Valaciclovir; Penciclovir (9-(4-hydroxy-3-hydroxymethyl-but-1-yl)guanine); Famciclovir (diacetyl ester of 9-(4-hydroxy-3-hydroxymethyl-but-1-yl)-6-deoxyguanine); Gancyclovir (9-(1,3-dihydroxy-2-Ara-A (adenosine arabinoside); Zidovudine (3′-azido-2′,3′-dideoxythymidine); Cidofovir (1-[(S)-3-hydroxy-2-(phosphonomethoxy)propyl]cytosine dihydrate); Dideoxyinosine (2′,3′-dideoxyinosine); Zalcitabine (2′,3′-dideoxycytidine); Stavudine (2′,3′-didehydro-2′,3′-dideoxythymidine); Lamivudine ((−)-β-L-3′-thia-2′,3′-dideoxycytidine); Abacavir (1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]-2-cyclopentene-1-methanol succinate); Emtricitabine (−)-β-L-3′-thia-2′,3′-dideoxy-5-fluorocytidine); Tenofovir disoproxil (Fumarate salt of bis(isopropoxycarbonyloxymethyl) ester of (R)-9-(2-phosphonylmethoxypropyl)adenine); Bromovinyl deoxyuridine (Brivudin); Iodo-deoxyuridine (Idoxuridine); Trifluorothymidine (Trifluridine); Nevirapine (11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-b:2′,3′-f][1,4]diazepin-6-one); Delavirdine (1-(5-methanesulfonamido-1H-indol-2-yl-carbonyl)-4-[3-(1-methylethyl-amino)pyridinyl) piperazine monomethane sulfonated); Efavirenz ((−)6-chloro-4-cyclopropylethynyl-4-trifluoromethyl-1,4-dihydro-2H-3,1-benzoxazin-2-one); Foscarnet (trisodium phosphonoformate); Ribavirin (1-β-D-ribofuranosyl-1H-1,2,4-triazole-3-carboxamide); Raltegravir (N-[(4-Fluorophenyl)methyl]-1,6-dihydro-5-hydroxy-1-methyl-2-[1-methyl-1-[[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino]ethyl]-6-oxo-4-pyrimidinecarboxamide monopotassium salt); Neplanocin A; Fomivirsen; Saquinavir (SQ); Ritonavir ([5S-(5R,8R,10R,11R)]-10-hydroxy-2-methyl-5-(1-methylethyl)-1-[2-(methylethyl)-4-thiazolyl]-3,6-dioxo-8,11-bis(phenylmethyl)-2,4,7,12-tetraazatridecan-13-oic acid 5-thiazolylmethyl ester); Indinavir ([(1S,2R,5(S)-2,3,5-trideoxy-N-(2,3-dihydro-2-hydroxy-1H-inden-1-yl)-5-[2-[[(1,1-dimethylethyl)amino]carbonyl]-4-pyridinylmethyl)-1-piperazinyl]-2-(phenylmethyl-erythro)pentonamide); Amprenavir; Nelfinavir; Lopinavir; Atazanavir; Bevirimat; Indinavir; Relenza; Zanamivir; Oseltamivir; Tarvacin; etc. are administered to individuals in a formulation (e.g., in the same or in separate formulations) with a pharmaceutically acceptable excipient(s).
[0280] In another aspect of the present invention, a pharmaceutical composition is provided, comprising, or consisting essentially of, a compound of the present invention, or a pharmaceutically acceptable salt, isomer, tautomer or prodrug thereof, and further comprising one or more additional anti-viral agents of interest. Any convenient anti-viral agents can be utilized in the subject methods in conjunction with the subject compounds. In some instances, the additional agent is an anti-HCV therapeutic agent selected from: an HCV NS3 protease inhibitor, an HCV NS5B RNA-dependent RNA polymerase inhibitor, a thiazolide, a sustained release thiazolide, a nucleoside analog, an interferon-alpha or lambda, a pegylated interferon, ribavirin, levovirin, viramidine, a TLR7 agonist, a TLR9 agonist, a cyclophilin inhibitor, an alpha-glucosidase inhibitor, an NS5A inhibitor, an NS3 helicase inhibitor, clemizole or clemizole analog (such as the benzimidizole and indazole analogs described in U.S. patent application Ser. Nos. 12/383,071 and 12/383,030), or other NS4B inhibitor including an NS4B amphipathic helix inhibitor. The subject compound and second antiviral agent, as well as additional therapeutic agents as described herein for combination therapies, can be administered orally, subcutaneously, intramuscularly, intranasally, parenterally, or other route. The subject compound and second antiviral agent may be administered by the same route of administration or by different routes of administration. The therapeutic agents can be administered by any suitable means including, but not limited to, for example, oral, rectal, nasal, topical (including transdermal, aerosol, buccal and sublingual), vaginal, parenteral (including subcutaneous, intramuscular, intravenous and intradermal), intravesical or injection into an affected organ. In certain cases, the therapeutic agents can be administered intranasally.
[0281] In some embodiments, the subject compound and an antimalarial agent, e.g., chloroquine, primaquine, mefloquine, doxycycline, atovaquone-proguanil, quinine, quinidine, artesunate, artemether, lumefantrine; etc. are administered to individuals in a formulation (e.g., in the same or in separate formulations) with a pharmaceutically acceptable excipient(s). The subject compound and second antimalarial agent, as well as additional therapeutic agents as described herein for combination therapies, can be administered orally, subcutaneously, intramuscularly, parenterally, or other route. The subject compound and second antimalarial agent may be administered by the same route of administration or by different routes of administration. The therapeutic agents can be administered by any suitable means including, but not limited to, for example, oral, rectal, nasal, topical (including transdermal, aerosol, buccal and sublingual), vaginal, parenteral (including subcutaneous, intramuscular, intravenous and intradermal), intravesical or injection into an affected organ.
[0282] The subject compounds may be administered in a unit dosage form and may be prepared by any methods well known in the art. Such methods include combining the subject compound with a pharmaceutically acceptable carrier or diluent which constitutes one or more accessory ingredients. A pharmaceutically acceptable carrier is selected on the basis of the chosen route of administration and standard pharmaceutical practice. Each carrier must be “pharmaceutically acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the subject. This carrier can be a solid or liquid and the type is generally chosen based on the type of administration being used.
[0283] Examples of suitable solid carriers include lactose, sucrose, gelatin, agar and bulk powders. Examples of suitable liquid carriers include water, pharmaceutically acceptable fats and oils, alcohols or other organic solvents, including esters, emulsions, syrups or elixirs, suspensions, solutions and/or suspensions, and solution and or suspensions reconstituted from non-effervescent granules and effervescent preparations reconstituted from effervescent granules. Such liquid carriers may contain, for example, suitable solvents, preservatives, emulsifying agents, suspending agents, diluents, sweeteners, thickeners, and melting agents. Preferred carriers are edible oils, for example, corn or canola oils. Polyethylene glycols, e.g. PEG, are also good carriers.
[0284] Any drug delivery device or system that provides for the dosing regimen of the instant disclosure can be used. A wide variety of delivery devices and systems are known to those skilled in the art.
[0285] Although such may not be necessary, compounds and agents described herein can optionally be targeted to the liver, using any known targeting means. The compounds of the disclosure may be formulated with a wide variety of compounds that have been demonstrated to target compounds to hepatocytes. Such liver targeting compounds include, but are not limited to, asialoglycopeptides; basic polyamino acids conjugated with galactose or lactose residues; galactosylated albumin; asialoglycoprotein-poly-L-lysine) conjugates; lactosaminated albumin; lactosylated albumin-poly-L-lysine conjugates; galactosylated poly-L-lysine; galactose-PEG-poly-L-lysine conjugates; lactose-PEG-poly-L-lysine conjugates; asialofetuin; and lactosylated albumin.
[0286] The terms “targeting to the liver” and “hepatocyte targeted” refer to targeting of a compound to a hepatocyte, particularly a virally infected hepatocyte, such that at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, or at least about 90%, or more, of the compound administered to the subject enters the liver via the hepatic portal and becomes associated with (e.g., is taken up by) a hepatocyte.
[0287] HCV infection is associated with liver fibrosis and in certain embodiments the inhibitors may be useful in treating liver fibrosis (particularly preventing, slowing of progression, etc.). The methods involve administering an compound of the disclosure as described above, in an amount effective to reduce viral load, thereby treating liver fibrosis in the subject. Treating liver fibrosis includes reducing the risk that liver fibrosis will occur; reducing a symptom associated with liver fibrosis; and increasing liver function.
[0288] Whether treatment with a compound as described herein is effective in reducing liver fibrosis is determined by any of a number of well-established techniques for measuring liver fibrosis and liver function. The benefit of anti-fibrotic therapy can be measured and assessed by using the Child-Pugh scoring system which comprises a multi-component point system based upon abnormalities in serum bilirubin level, serum albumin level, prothrombin time, the presence and severity of ascites, and the presence and severity of encephalopathy. Based upon the presence and severity of abnormality of these parameters, patients may be placed in one of three categories of increasing severity of clinical disease: A, B, or C.
[0289] Treatment of liver fibrosis (e.g., reduction of liver fibrosis) can also be determined by analyzing a liver biopsy sample. An analysis of a liver biopsy comprises assessments of two major components: necroinflammation assessed by “grade” as a measure of the severity and ongoing disease activity, and the lesions of fibrosis and parenchymal or vascular remodeling as assessed by “stage” as being reflective of long-term disease progression. See, e.g., Brunt (2000) Hepatol. 31:241-246; and METAVIR (1994) Hepatology 20:15-20. Based on analysis of the liver biopsy, a score is assigned. A number of standardized scoring systems exist which provide a quantitative assessment of the degree and severity of fibrosis. These include the METAVIR, Knodell, Scheuer, Ludwig, and Ishak scoring systems.
[0290] The METAVIR scoring system is based on an analysis of various features of a liver biopsy, including fibrosis (portal fibrosis, centrilobular fibrosis, and cirrhosis); necrosis (piecemeal and lobular necrosis, acidophilic retraction, and ballooning degeneration); inflammation (portal tract inflammation, portal lymphoid aggregates, and distribution of portal inflammation); bile duct changes; and the Knodell index (scores of periportal necrosis, lobular necrosis, portal inflammation, fibrosis, and overall disease activity). The definitions of each stage in the METAVIR system are as follows: score: 0, no fibrosis; score: 1, stellate enlargement of portal tract but without septa formation; score: 2, enlargement of portal tract with rare septa formation; score: 3, numerous septa without cirrhosis; and score: 4, cirrhosis.
[0291] Knodell's scoring system, also called the Hepatitis Activity Index, classifies specimens based on scores in four categories of histologic features: I. Periportal and/or bridging necrosis; II. Intralobular degeneration and focal necrosis; III. Portal inflammation; and IV. Fibrosis. In the Knodell staging system, scores are as follows: score: 0, no fibrosis; score: 1, mild fibrosis (fibrous portal expansion); score: 2, moderate fibrosis; score: 3, severe fibrosis (bridging fibrosis); and score: 4, cirrhosis. The higher the score, the more severe the liver tissue damage. Knodell (1981) Hepatol. 1:431.
[0292] In the Scheuer scoring system scores are as follows: score: 0, no fibrosis; score: 1, enlarged, fibrotic portal tracts; score: 2, periportal or portal-portal septa, but intact architecture; score: 3, fibrosis with architectural distortion, but no obvious cirrhosis; score: 4, probable or definite cirrhosis. Scheuer (1991) J. Hepatol. 13:372.
[0293] The Ishak scoring system is described in Ishak (1995) J. Hepatol. 22:696-699. Stage 0, No fibrosis; Stage 1, Fibrous expansion of some portal areas, with or without short fibrous septa; stage 2, Fibrous expansion of most portal areas, with or without short fibrous septa; stage 3, Fibrous expansion of most portal areas with occasional portal to portal (P-P) bridging; stage 4, Fibrous expansion of portal areas with marked bridging (P-P) as well as portal-central (P-C); stage 5, Marked bridging (P-P and/or P-C) with occasional nodules (incomplete cirrhosis); stage 6, Cirrhosis, probable or definite.
[0294] In some embodiments, a therapeutically effective amount of a compound of the disclosure is an amount of compound that effects a change of one unit or more in the fibrosis stage based on pre- and post-therapy measures of liver function (e.g., as determined by biopsies). In particular embodiments, a therapeutically effective amount of the subject compound reduces liver fibrosis by at least one unit in the Child-Pugh, METAVIR, the Knodell, the Scheuer, the Ludwig, or the Ishak scoring system.
[0295] Secondary, or indirect, indices of liver function can also be used to evaluate the efficacy of treatment. Morphometric computerized semi-automated assessment of the quantitative degree of liver fibrosis based upon specific staining of collagen and/or serum markers of liver fibrosis can also be measured as an indication of the efficacy of a subject treatment method. Secondary indices of liver function include, but are not limited to, serum transaminase levels, prothrombin time, bilirubin, platelet count, portal pressure, albumin level, and assessment of the Child-Pugh score. An effective amount of the subject compound is an amount that is effective to increase an index of liver function by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, or at least about 80%, or more, compared to the index of liver function in an untreated individual, or to a placebo-treated individual. Those skilled in the art can readily measure such indices of liver function, using standard assay methods, many of which are commercially available, and are used routinely in clinical settings.
[0296] Serum markers of liver fibrosis can also be measured as an indication of the efficacy of a subject treatment method. Serum markers of liver fibrosis include, but are not limited to, hyaluronate, N-terminal procollagen III peptide, 7S domain of type IV collagen, C-terminal procollagen I peptide, and laminin. Additional biochemical markers of liver fibrosis include α-2-macroglobulin, haptoglobin, gamma globulin, apolipoprotein A, and gamma glutamyl transpeptidase.
[0297] In some cases, a therapeutically effective amount of the subject compound is an amount that is effective to reduce a serum level of a marker of liver fibrosis by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, or at least about 80%, or more, compared to the level of the marker in an untreated individual, or to a placebo-treated individual. Those skilled in the art can readily measure such serum markers of liver fibrosis, using standard assay methods, many of which are commercially available, and are used routinely in clinical settings. Methods of measuring serum markers include immunological-based methods, e.g., enzyme-linked immunosorbent assays (ELISA), radioimmunoassays, and the like, using antibody specific for a given serum marker.
[0298] Qualitative or quantitative tests of functional liver reserve can also be used to assess the efficacy of treatment with an agent. These include: indocyanine green clearance (ICG), galactose elimination capacity (GEC), aminopyrine breath test (ABT), antipyrine clearance, monoethylglycine-xylidide (MEG-X) clearance, and caffeine clearance.
[0299] As used herein, a “complication associated with cirrhosis of the liver” refers to a disorder that is a sequellae of decompensated liver disease, i.e., or occurs subsequently to and as a result of development of liver fibrosis, and includes, but it not limited to, development of ascites, variceal bleeding, portal hypertension, jaundice, progressive liver insufficiency, encephalopathy, hepatocellular carcinoma, liver failure requiring liver transplantation, and liver-related mortality.
[0300] A therapeutically effective amount of a compound in this context can be regarded as an amount that is effective in reducing the incidence (e.g., the likelihood that an individual will develop) of a disorder associated with cirrhosis of the liver by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, or at least about 80%, or more, compared to an untreated individual, or to a placebo-treated individual.
[0301] Whether treatment with the subject compound is effective in reducing the incidence of a disorder associated with cirrhosis of the liver can readily be determined by those skilled in the art.
[0302] Reduction in HCV viral load, as well as reduction in liver fibrosis, can be associated with an increase in liver function. Thus, the disclosure provides methods for increasing liver function, generally involving administering a therapeutically effective amount of a compound of the disclosure. Liver functions include, but are not limited to, synthesis of proteins such as serum proteins (e.g., albumin, clotting factors, alkaline phosphatase, aminotransferases (e.g., alanine transaminase, aspartate transaminase), 5′-nucleosidase, γ-glutaminyltranspeptidase, etc.), synthesis of bilirubin, synthesis of cholesterol, and synthesis of bile acids; a liver metabolic function, including, but not limited to, carbohydrate metabolism, amino acid and ammonia metabolism, hormone metabolism, and lipid metabolism; detoxification of exogenous drugs; a hemodynamic function, including splanchnic and portal hemodynamics; and the like.
[0303] Whether a liver function is increased is readily ascertainable by those skilled in the art, using well-established tests of liver function. Thus, synthesis of markers of liver function such as albumin, alkaline phosphatase, alanine transaminase, aspartate transaminase, bilirubin, and the like, can be assessed by measuring the level of these markers in the serum, using standard immunological and enzymatic assays. Splanchnic circulation and portal hemodynamics can be measured by portal wedge pressure and/or resistance using standard methods. Metabolic functions can be measured by measuring the level of ammonia in the serum.
[0304] Whether serum proteins normally secreted by the liver are in the normal range can be determined by measuring the levels of such proteins, using standard immunological and enzymatic assays. Those skilled in the art know the normal ranges for such serum proteins. The following are non-limiting examples. The normal range of alanine transaminase is from about 7 to about 56 units per liter of serum. The normal range of aspartate transaminase is from about 5 to about 40 units per liter of serum. Bilirubin is measured using standard assays. Normal bilirubin levels are usually less than about 1.2 mg/dL. Serum albumin levels are measured using standard assays. Normal levels of serum albumin are in the range of from about 35 to about 55 g/L. Prolongation of prothrombin time is measured using standard assays. Normal prothrombin time is less than about 4 seconds longer than control.
[0305] A therapeutically effective amount of a compound in this context is one that is effective to increase liver function by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or more. For example, a therapeutically effective amount of a compound is an amount effective to reduce an elevated level of a serum marker of liver function by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or more, or to reduce the level of the serum marker of liver function to within a normal range. A therapeutically effective amount of a compound is also an amount effective to increase a reduced level of a serum marker of liver function by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or more, or to increase the level of the serum marker of liver function to within a normal range.
[0306] HCV infection is associated with hepatic cancer and in certain embodiments the present disclosure provides compositions and methods of reducing the risk that an individual will develop hepatic cancer. The methods involve administering the subject compound, as described above, wherein viral load is reduced in the individual, and wherein the risk that the individual will develop hepatic cancer is reduced. An effective amount of a compound is one that reduces the risk of hepatic cancer by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, or more. Whether the risk of hepatic cancer is reduced can be determined in, e.g., study groups, where individuals treated according to the subject methods have reduced incidence of hepatic cancer.
Subjects Amenable to Treatment Using the Compounds of the Disclosure
[0307] Individuals who have been clinically diagnosed as infected with a pathogen of interest are suitable for treatment with the methods of the present disclosure. In particular embodiments of interest, individuals of interest for treatment according to the disclosure have detectable pathogen titer indicating active replication, for example an HCV titer of at least about 10.sup.4, at least about 10.sup.5, at least about 5×10.sup.5, or at least about 10.sup.6, or greater than 2 million genome copies of HCV per milliliter of serum. Similar methods may be used to determine whether subjects infected with another pathogen are suitable for treatment using the subject methods.
[0308] The effectiveness of the anti-infective treatment may be determined using any convenient method. For example, whether a subject method is effective in treating a virus infection can be determined by measuring viral load, or by measuring a parameter associated with infection.
[0309] Viral load can be measured by measuring the titer or level of virus in serum. These methods include, but are not limited to, a quantitative polymerase chain reaction (PCR) and a branched DNA (bDNA) test. Many such assays are available commercially, including a quantitative reverse transcription PCR (RT-PCR) (Amplicor HCV Monitor™, Roche Molecular Systems, New Jersey); and a branched DNA (deoxyribonucleic acid) signal amplification assay (Quantiplex™ HCV RNA Assay (bDNA), Chiron Corp., Emeryville, Calif.). See, e.g., Gretch et al. (1995) Ann. Intern. Med. 123:321-329.
EXAMPLES
[0310] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use embodiments of the present disclosure, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.
[0311] While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present disclosure. All such modifications are intended to be within the scope of the claims appended hereto.
Example 1: Synthesis and Assays
[0312] In the assays described here, p110α-p85 complex and p110γ were acquired from Millipore. Assays were performed with La-phosphatidylinositol (Avanti) as described in Knight et al. Nat Protoc. 2007; 2 (10):2459-66. Inhibitor series were prepared 10% DMSO as 5× stocks for the assay. Assays of HsVps34 were performed as described in Knight et al, except that the final assay buffer composition used was changed to 20 mM HEPES 7.5, 100 mM NaCl, 3 mM MgCl, 1 mg/mL PI and 44 nM hvps34 was used in the assay. For inhibitors with an apparent IC50 less than or equal to 22 nM, values were reassayed using 4.4 nM hvps34 with 3 mM MnCl.sub.2. COS-7 cells were cultured in 10 cm dishes and transfected at 70% confluence with 10 μg of plasmid DNA (HA-tagged bovine PI4KIIIβ, HA-tagged human PI4KIIIα) using Lipofectamine 2000 and 5 ml Opti-MEM following the manufacturer's instructions. After 5 hours the transfection medium was replaced with 10 ml complete DMEM. 36 hrs post transfection, cells were washed once with 5 ml PBS (pH 7.4) and lysed in 1 ml of lysis buffer (1) on ice. Lysates were collected by scraping and after 15 min they were centrifuged at 13,000 rpm for 10 min. To the lysates was added 200 μl of protein G Sepharose 4 fast flow beads that were prewashed with PBS and lysis buffer and 2 μg of anti-HA antibody. The tubes were then incubated overnight at 4 degrees C. in a tube rotator. The Sepharose beads in the lysate were washed twice with 150 mM NaCl in RIPA buffer, twice with RIPA buffer and once with kinase buffer (50 mM Tris/HCl, pH 7.5, 20 mM MgCl2, 1 mM EGTA, 1 mM PtdIns, 0.4% Triton X-100, 0.5 mg/mL BSA) and finally the beads were resuspended in 200 μL kinase buffer. Kinase reactions were run in a mixture of 45 μL of PI buffer (1 mM PI in kinase buffer), 10 μL of immunoprecipitated beads, 2 □L of inhibitors (dissolved and diluted in DMSO) or DMSO and 5 μL of [γ-.sup.32P]-ATP (1 mM and 2 μCi/tube). The immunoprecipitates in PI buffer were pre-incubated with the drugs for 20 min prior the initiation of kinase reaction by adding ATP and the reactions were carried out for 30 min in 15 ml polypropolyne tubes. Reactions were terminated by addition of 3 ml of CHCl.sub.3:CH.sub.3OH:HCl (200:100:0.75) followed by 0.6 ml of 0.6N HCl to induce phase separation. The mixtures were vortexed, centrifuged at 2000 rpm for 2 min and the upper phase was discarded. To the lower phase was added 1.5 ml of CHCl.sub.3:CH.sub.3OH:0.6N HCl (3:48:47) and the mixture vortexed and centrifuged at 2000 rpm for 2 min. The lower phase was then transferred to counting vials and evaporated. Samples were counted in a scintillation beta counter after adding 5 ml of Instafluor (Perkin-Elmer).
[0313] Synthesis: Compounds may be synthesized using any convenient method. For example, by similar methods to those described by Shokat et al. “A pharmacological map of the PI3-K family defines a role for p110alpha in insulin signaling.” Cell. 2006; 125(4):733-47. Starting materials are obtained from Aldrich or Alfa Aesar. Reactions are monitored by LC/MS and reaction products characterized by LC/MS and 1H NMR. Intermediates and final products are purified by silica gel chromatography or by reverse phase HPLC.
[0314] Exemplary synthetic schemes 1-3, which can be adapted for the synthesis of subject compounds, are shown below:
##STR00445## ##STR00446##
##STR00447## ##STR00448##
##STR00449## ##STR00450##
[0315] PI-kinase assay: Compounds are tested in C.1.1. PI kinase assays as described by Shokat et al., “A membrane capture assay for lipid kinase activity.” Nat. Protoc. 2007; 2(10):2459-66.
[0316] Anti-HCV assay: Anti-HCV assays are performed as described by Cho et al. “Identification of a class of HCV inhibitors directed against the nonstructural protein NS4B.” Sci. Transl. Med. 2011; 2(15):15ra6.
[0317] Broad-spectrum anti-infective assays: Compounds are tested for activity against selected agents harboring proteins with BAAPP domains, or other PI-4 or PIP2 binding motifs, (i.e. Vaccinia virus, Japanese encephalitis virus, hepatitis A virus, and influenza virus) in clinical studies. Activity against multiple NIAID Category A, B, and C pathogens is assayed.
[0318] Vaccinia virus assay: Standard plaque assays are performed on CV-1 cells, using methods described by Glenn et al., “Amphipathic helix-dependent localization of NS5A mediates hepatitis C virus RNA replication.” J. Virol. 2003; 77(10):6055-61, in the presence of vehicle or vehicle plus various concentrations of compound.
[0319] HAV assay: Huh7 cells harboring HAV replicons encoding a blasticidin resistance gene (Yang et al., “Disruption of innate immunity due to mitochondrial targeting of a picornaviral protease precursor.” Proc Natl Acad Sci USA 2007; 104(17):7253-8) is grown in media containing blasticidin, with or without various concentrations of compound. Anti-HAV activity is assessed by both cell plating efficiency and HAV RNA levels using quantitative RT-PCR assays. A luciferase-linked HAV replicon for transient replication assays is used to evaluate the effects of HAV BAAPP domain mutants.
[0320] JEV assay: JEV assays are performed using both infectious virus in cell culture, as well as in an in vivo animal model, using similar methods to those described by Shah et al. “Molecular characterization of attenuated Japanese encephalitis live vaccine strain ML-17.” Vaccine. 2006; 24(4):402-11.
[0321] Influenza virus assay: Influenza virus assays are performed using infectious virus in cell culture, using similar methods to those described by Hossain et al. “Establishment and characterization of a Madin-Darby canine kidney reporter cell line for influenza A virus assays.” J. Clin. Microbiol. 48(7):2515-23.
[0322] Plasmodium falciparum assay: Plasmodium falciparum assays are performed using an erythrocyte-fed culture of P. falciparum ring forms, using similar methods to those described by Deu et al. “Functional Studies of Plasmodium falciparum Dipeptidyl Aminopeptidase I Using Small Molecule Inhibitors and Active Site Probes.” Chemistry & Biology 17, 808-819.
[0323] Rhinovirus assay: Rhinovirus assays are performed by determining to what extent the compound protects HeLa S3 cells from the cytopathic effect of an inoculum of human rhinovirus 14, using similar methods to those described by Buckwold et al., “Synergistic In Vitro Interactions between Alpha Interferon and Ribavirin against Bovine Viral Diarrhea Virus and Yellow Fever Virus as Surrogate Models of Hepatitis C Virus Replication,” Antimicrobial Agents and Chemotherapy 47(7), 2293-2298.
[0324] HAV assay: HAV assays are performed by co-culturing Huh7-derived cells harboring the blasticidin-selectable HAV replicon (HAV-Bla, described by Yang et al, “Disruption of innate immunity due to mitochondrial targeting of a picornaviral protease precursor”, PNAS 104(17), 7253-7258) for over two weeks in DMEM with 10% FBS, 1% Pen-Strep, 1% L-Glutamine, 1% nonessential amino acids, and 4 μg/mL blasticidin, with various concentrations of compound or vehicle control in 6-well plates at a density of 1000 HAV-Bla cells per well and 1/72 confluent plate worth of Huh7 feeder cells per well. At the end of this culture, large colonies in each well are counted and an effective concentration at which plating efficiency is decreased by 50% (EC50) is calculated.
[0325] For all of the assays described above, EC50, EC90, and CC50 values are determined, and experiments are performed starting drug treatments at various times post initiation of infection to help localize the most sensitive aspects of each pathogen's life cycle to PI4-kinase inhibition.
[0326] Resistance assays: The capacity for emergence of resistance and its nature is determined using any convenient methods, for example methods that involve sequencing of any resistant isolates that are able to be propagated. Co-treatments with other drugs are also performed. Experiments are conducted under BL2+ conditions where appropriate.
[0327] Humanized mouse model: The performance characteristics of the compounds are assessed by dosing the compounds in a mouse model with a humanized liver to determine their in vivo pharmacokinetic (PK) and pharmacodynamic properties. This model consists of immunodeficient NOG mice (NOD/shi SCID Il2rg −/−) harboring a Herpes virus-derived thymidine kinase (TK) transgene under the control of an albumin promoter (Hasegawa et al., “The reconstituted ‘humanized liver’ in TK-NOG mice is mature and functional.” Biochem Biophys Res Commun. 2011; 405(3):405-10). A brief exposure to ganciclovir targets destruction of the endogenous mouse liver, which is followed by the transplantation of human liver cells. High level engraftment of human hepatocytes can be achieved and efficient HCV infection established. A quantitative analysis of in vivo PK parameters and efficacy of the compounds and metabolites in the plasma of the humanized mice is performed.
[0328] PK and PD: Cohorts of humanized TK-NOG mice (e.g. 5 mice per treatment group) are gavaged with one dose of compound. Doses are chosen so as to maintain a concentration above the respective EC50s. Serial aliquots of plasma are obtained at baseline, 15 minutes, 30 minutes, 1 hr and 2 hr post dosing. Similarly treated groups of mice are sacrificed to analyze levels of the drugs and key metabolites in the liver. Concentrations of compounds and their metabolites are measured. PK parameters, such as Cmax, T½, AUC, and oral clearance are determined. Based on these parameters, cohorts of humanized TK-NOG mice (5 mice per treatment group) infected with HCV inoculums consisting of the infectious 2a clone (25) or de-identified patient-derived sera are gavaged (Glenn et al., “In vivo antiviral efficacy of prenylation inhibitors against hepatitis delta virus (HDV).” Journal of Clinical Investigation. 2003; 112(3):407-14) for multiple doses and serial serum aliquots are obtained and antiviral efficacy determined by measuring HCV titers by quantitative real-time PCR. Individually-treated mice can also serve as their own control wherein the HCV titers before, during, and after treatment can be used to assess antiviral efficacy wherein an antiviral effect in indicated by a drop in titer during the treatment phase compared to the pretreatment phase, with (in the case where the virus has not been completely eliminated during the treatment period) or without (in the case where the virus has been completely eliminated during the treatment period) an increase in titer following cessation of treatment.
[0329] Assessment of drug resistance: (In vitro) Huh7 cells harboring a bicistronic genotype 1b subgenomic replicon, wherein the first cistron encodes the neomycinphosphotransferase gene (which confers resistance to G418) and the second cistron encodes the HCV non-structural proteins required for RNA genome replication, are grown in media containing G418 plus increasing concentrations of compounds to select for drug resistant colonies. This, along with extraction of the replicons harbored in the resistant cells, sequencing to identify candidate resistance mutations, and cloning of these mutations back into a wild-type replicon to confirm they are truly causative of the resistance, is performed using convenient methods. In vivo) Inoculums consist of the infectious 2a clone and de-identified patient-derived sera. Once establishment of infection has been confirmed, humanized mice are treated by oral gavage with a resistance-promoting regimen of compounds involving progressive dose escalation from a low dose (0.1 mg/kg/day), with drug holidays. Serum samples for analysis are taken at time 0, and serially thereafter on a weekly basis. The focus is first on any samples that display a rebound in titer of greater than 1 log after a previous nadir. Standard DNA sequencing of individual clones isolated from RT-PCR cloning is performed. Ultradeep pyrosequencing is reserved to determine earliest evidence of any observed resistance. As a control, similar experiments with an HCV NS3 protease inhibitor (e.g. Boceprevir) are performed.
Example 2
[0330] Selected compounds of Table 1 and 2 were prepared and tested for inhibition activity in a variety of kinase assays.
TABLE-US-00008 TABLE 3 Comparison of PI4K and PI3K Kinase activity of select compounds PI3K PI3K Compound PI4KIIIA PI4KIIIB p110a p110g PI3KC2B PI3KC2G S-1 A D D D A S-8 B S-9 A S-25 B S-28 C S-29 B S-37 B S-41 A S-43 B S-46 B S-49 A S-50 B S-52 B S-53 B S-54 C S-78 C S-81 B S-91 B S-92 C S-94 C S-95 B S-98 D A D D S-100 D B D C S-101 C S-102 B S-103 C S-107 C S-109 B S-111 B S-115 A S-118 B S-119 B S-121 C S-122 B S-123 A S-127 D B D D S-128 D B D D S-129 D B D D S-131 D B D S-133 A S-134 A S-135 A S-136 A S-138 B S-145 B A D D S-146 B S-147 B A D D S-148 B A D D S-149 A S-150 B S-151 A S-152 A S-153 A S-154 B S-155 B S-156 A S-157 B S-159 B S-160 A D D B S-161 B S-185 A S-166 A S-167 A S-169 A A D D D S-170 A A D D D S-173 A S-178 B S-183 A S-184 B S-185 C S-188 A S-189 A S-192 B S-193 A D D S-194 B S-195 B S-196 B S-197 A S-198 B S-199 A S-200 B S-201 A S-202 A S-203 A S-204 B S-205 B S-206 C S-207 A S-208 B S-209 B S-210 C S-214 D B D D S-215 C A D D C S-216 A D D C S-218 A S-219 A S-220 A S-221 A S-222 A S-223 A S-226 A S-227 A D D D C S-228 B S-229 B S-230 A S-231 A D D B S-234 B S-235 B S-253 B S-258 C S-259 A A C C C S-260 A A D D D S-261 A A B B B S-262 A A D C B S-263 A A C C B S-265 A A D D C A = <100 nM B = 100 nM-1 uM C = 1-0 uM D = >10 uM
Example 3: Activity of Exemplary Compound
[0331] ##STR00451##
[0332] Compound 1 shown above exhibits activity against both PI4KIIIα (IC50 1.75 micromolar) and PI4KIIIβ (IC50 7 nanomolar) in in vitro enzyme assays.
[0333] To further confirm its mechanism of action the effect of (1) on PI-4 levels was determined in cells using immunofluorescence to monitor the intracellular localized pools of PI-4. The effect of (1) on intracellular pools of PIP2 was tested, which were predicted to be similarly sensitive to inhibition using (1). Indeed, a dose-dependent decrease in PI-4 and PIP2 was observed upon treatment with (1). As a control for non-specific effects on the cells, the latter were also co-stained with an antibody to ER-localized calnexin, which revealed that the effect on PI-4 and PIP2 occurred in the absence of any detectable effects on the ER.
[0334] Cell images show that (1) decreases PI(4)P and PI(4,5)P.sub.2 (bottom panels) in a dose-dependent manner. Uninfected Huh7.5 cells or HCV-infected Huh7.5 cells were used. Cells were treated with 250 nm, 500 nM or 1 uM concentrations of (1) or vehicle control, and analyzed by immunofluorescence with antibodies to PI(4)P or PI(4,5)P.sub.2 along with an antibody to calnexin to control for ER morphology.
[0335] The concentrations at which significant effects on PI-4 and PIP2 were observed in the target cells parallel the observed EC50 of 365 nM (CC50>10 micromolar) for PT423 against HCV in standard replication assays (Cho et al., “Identification of a class of HCV inhibitors directed against the nonstructural protein NS4B.” Sci. Transl. Med. 2011; 2(15):15ra6). Consistent with its host PI4-target, resistance was not able to be selected using the HCV replicon system.
Example 4
[0336] Tables 4-6 show the results of testing selected compounds for anti-viral (EC.sub.50) activity in various assays, such as a HCV genotype 2a in Huh7.5 cells by luciferase reporter assay, for cell toxicity (CC.sub.50) and metabolic halflife (t½), according to the methods described above.
TABLE-US-00009 TABLE 4 Comparison of antiviral activity of select PI4K inhibitors. HCV2a HRV EV71 Ebola Norovirus HuH-7 Compound EC.sub.50 EC.sub.50 EC.sub.50 EC.sub.50 EC.sub.50 CC.sub.50 S-1 B A E S-29 A E S-32 D A D E S-66 D A E S-85 A E S-89 A E S-98 D A A D E S-106 A E S-115 C A E S-138 C A E S-227 B B A C C E S-228 C A D E S-260 C D E S-261 B D E S-263 B D E A = <1 nM B = 1-100 nM C = 100 nM-1 uM D = 1-10 uM E = >10 uM
TABLE-US-00010 TABLE 5 Comparison of antiviral activity of select PI4K inhibitors. A = <1 nM; B = 1-100 nM; C = 100 nM-1 uM; D = 1-10 uM; E = >10 uM Compound EV71 EC.sub.50 (μM) HRV EC.sub.50 (μM) S-315 B B S-316 B B S-317 B B S-318 A B S-319 B B S-320 B B S-321 B B S-322 B B S-323 A A S-328 B B S-327 B B S-326 B C S-325 D D S-324 B B S-329 B B S-334 B B S-375 B B S-335 B B S-330 C D S-333 C C S-336 B B S-337 B C S-338 B B S-339 B B S-341 B B S-331 B B S-340 B B
Compounds of interest were tested in a variety of cell based assays for antiviral activity.
TABLE-US-00011 TABLE 6 Antiviral activity of PI4K inhibitors. A = <1 nM; B = 1-100 nM; C = 0.1-1 uM; D = 1-10 uM; E = >10 uM Compound S-98 S-227 S-316 S-328 Coxsackie virus B3 EC.sub.50 (uM) B B <B <B Enterovirus 68 EC.sub.50 (uM) A A <B <B Enterovirus 71 EC.sub.50 (uM) B B <B <B Poliovirus (WM-3) EC.sub.50 (uM) <B <B C <B NV (GT1) EC.sub.50 (uM) D C Adenovirus 5 (Adenoid 75) EC.sub.50 (uM) E E E E Dengue virus 2 EC.sub.50 (uM) E E >D >E Influenza A virus H1N1 EC.sub.50 (uM) E E >D >E MERS coronavirus EC.sub.50 (uM) E E >D >E
[0337] Notwithstanding the appended claims, the disclosure set forth herein is also described by the following clauses.
Clause 1. A compound having the formula (XXI)
##STR00452##
wherein: R.sup.2 is an alkoxy (e.g., methoxy) or a substituted alkoxy; R.sup.3 is hydrogen, a lower alkyl (e.g., methyl) or a substituted lower alkyl; Y.sup.3 is CH or N; Z.sup.2 is absent, CO or SO.sub.2 (e.g., Z.sup.2 is absent or CO); R.sup.1 is an aryl, a substituted aryl (e.g., a substituted phenyl), a heteroaryl, a substituted heteroaryl, (e.g., a substituted pyridyl), an alkyl, a substituted alkyl, a cycloalkyl, a substituted cycloalkyl (e.g., a substituted cyclohexyl), a heterocycle (e.g., a tetrahydropyran or a piperidinyl) or a substituted heterocycle; and R.sup.4 is selected from alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkyl-cycloalkyl, substituted alkyl-cycloalkyl, aryl, substituted aryl, heterocycle, substituted heterocycle, alkyl-heterocycle (e.g., —CH.sub.2-(4-tetrahydropyran)) and substituted alkyl-heterocycle; or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
2. The compound of clause 1, having the formula (XXII):
##STR00453##
wherein: R.sup.10 is selected from cycloalkyl, substituted cycloalkyl, heterocycle (e.g., 4-tetrahydropyran) and substituted heterocycle; and R.sup.51 and R.sup.52 are independently selected from H, halogen (e.g., fluoro), alkyl (e.g., lower alkyl) and substituted alkyl.
3. The compound of clause 2, having the formula (XXIII):
##STR00454##
wherein: R.sup.31—R.sup.35 are independently selected from hydrogen, halogen (e.g., fluoro), alkyl, substituted alkyl, hydroxy, alkoxy, substituted alkoxy, acyl, substituted acyl and —CO.sub.2R, wherein R is H, alkyl or substituted alkyl.
4. The compound of clause 2 or 3, having the formula (XXIV) or formula (XXV):
##STR00455##
wherein one and only one of R.sup.33 and R.sup.34 is hydroxy.
5. The compound of clause 4, having any one of the formulae (XXVI)-(XXVIII):
##STR00456##
wherein: R.sup.31, R.sup.32, R.sup.34 and R.sup.35 are independently selected from hydrogen and halogen (e.g., fluoro); and (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro), and CO.sub.2R″ wherein R″ is hydrogen, alkyl or substituted alkyl.
6. The compound of clause 5, having one of the following structures:
##STR00457##
or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
7. The compound of clause 3, having formula (XIX):
##STR00458##
wherein: R.sup.31—R.sup.35 are independently selected from hydrogen and halogen (e.g., fluoro or chloro), wherein 0, 1 or 2 of R.sup.31—R.sup.35 are halogen; and (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro), and CO.sub.2R″ wherein R″ is hydrogen, alkyl or substituted alkyl.
8. The compound of clause 2, having formula (XXX):
##STR00459##
wherein: R.sup.4 is a lower alkyl or a substituted lower alkyl (e.g., an isopropyl); and (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro), and CO.sub.2R″ wherein R″ is hydrogen, alkyl or substituted alkyl.
9. The compound of clause 2, having the formula (XXXI):
##STR00460##
wherein: each (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen (e.g., fluoro or chloro) and CO.sub.2R″ wherein R″ is hydrogen, alkyl or substituted alkyl.
10. The compound of clause 9, having the structure:
##STR00461##
or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
11. The compound of clause 3, having the formula (XXXII):
##STR00462##
wherein R.sup.31—R.sup.33 and R.sup.35 are independently selected from hydrogen and halogen; (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen and CO.sub.2R″ wherein R″ is hydrogen, alkyl or substituted alkyl; and R.sup.1 is H, alkyl or substituted alkyl.
12. The compound of clause 11, having the structure:
##STR00463##
wherein R′ is H or a lower alkyl; or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
13. The compound of clause 1, having the formula (XXXIII) or formula (XXXIV):
##STR00464##
wherein: R.sup.2 is an alkoxy (e.g., methoxy) or a substituted alkoxy; R.sup.3 is hydrogen, a lower alkyl (e.g., methyl) or a substituted lower alkyl; R.sup.1 is an aryl, a substituted aryl, (e.g., a substituted phenyl), a heteroaryl, a substituted heteroaryl, (e.g., a substituted pyridyl), a cycloalkyl, a substituted cycloalkyl (e.g., a substituted cyclohexyl), a heterocycle (e.g., a tetrahydropyran or a piperidinyl) or a substituted heterocycle; and R.sup.4 is selected from cycloalkyl, substituted cycloalkyl, alkyl-cycloalkyl, substituted alkyl-cycloalkyl, heterocycle, substituted heterocycle, alkyl-heterocycle (e.g., —CH.sub.2-(4-tetrahydropyran)) and substituted alkyl-heterocycle.
14. The compound of clause 13, having one of the formula (XXXV) and formula (XXXVI):
##STR00465##
wherein: (R).sub.n is one or more optional substituents each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen and CO.sub.2R″ wherein R″ is hydrogen, alkyl or substituted alkyl.
15. The compound of clause 14, having one of the formula (XXXVII) and formula (XXXVIII):
##STR00466##
wherein: R.sup.31—R.sup.35 are independently selected from hydrogen, halogen (e.g., fluoro), alkyl, substituted alkyl, hydroxy, alkoxy, substituted alkoxy, acyl, substituted acyl and —CO.sub.2R, wherein R is H, alkyl or substituted alkyl.
16. The compound of clause 15, wherein R.sup.31—R.sup.35 are independently selected from hydrogen, methyl, halogen (e.g., fluoro or chloro) and hydroxy.
17. The compound of clause 15 or 16, wherein R.sup.31 and R.sup.35 are independently lower alkyl or substituted lower alkyl (e.g., methyl).
18. The compound of clause 17, having the structure:
##STR00467##
or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
19. The compound of clause 1, having the formula (XXXIX):
##STR00468##
wherein R.sup.41 and R.sup.43 are independently hydrogen, a lower alkyl or a substituted lower alkyl (e.g., methyl); and R.sup.42 is selected from cycloalkyl, substituted cycloalkyl, alkyl-cycloalkyl, substituted alkyl-cycloalkyl, heterocycle, substituted heterocycle, alkyl-heterocycle (e.g., —CH.sub.2-(4-tetrahydropyran)) and substituted alkyl-heterocycle.
20. The compound of clause 19, having the formula (XL) or (XLI):
##STR00469##
wherein: Y.sup.11 and Y.sup.12 are selected from CR.sup.11 2, NR″ and O, wherein each R″ is independently H, R, an acyl or a substituted acyl; each R is independently H, an alkyl, a substituted alkyl, an alkoxy or a halogen (e.g., a fluoro); and n is 0, 1, 2, 3 or 4.
21. The compound of clause 20, having the formula (XLII) or (XLIII):
##STR00470##
22. The compound of clause 21, wherein Y.sup.11 and Y.sup.12 are each NH.
23. The compound of clause 21, wherein n is 0.
24. The compound of clause 21, wherein (R).sub.n is 4-CO.sub.2R′, wherein R.sup.1 is hydrogen or lower alkyl (e.g., ethyl).
25. The compound of clause 20, wherein: R.sup.41 is methyl; and R.sup.42 is selected from cyclohexyl, substituted cyclohexyl, —CH.sub.2-cyclohexyl and substituted —CH.sub.2-cyclohexyl.
26. The compound of clause 25, wherein the compound has one of the following structures:
##STR00471##
or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
27. The compound of clause 19, having one of the formulae (XLIVa)-(XLIVd) and (XLVa)-(XLVd):
##STR00472## ##STR00473##
wherein: R.sup.31—R.sup.35 are independently selected from hydrogen, halogen (e.g., fluoro or chloro), alkyl, substituted alkyl, hydroxy, alkoxy, substituted alkoxy, acyl, substituted acyl and —CO.sub.2R, wherein R is H, alkyl or substituted alkyl.
28. The compound of clause 27, having one of the formulae (XLVIa)-(XLVId) and (XLVIIa)-(XLVIId):
##STR00474## ##STR00475##
wherein: (R).sub.n is one or more optional substituents (i.e., n is 0, 1, 2, 3, 4 or 5) each independently selected from alkyl, substituted alkyl, hydroxyl, alkoxy, substituted alkoxy, halogen and CO.sub.2R″ wherein R″ is hydrogen, alkyl or substituted alkyl; Y.sup.4 is CH, CR or O; and R.sup.41 is H, lower alkyl or substituted lower alkyl.
29. The compound of clause 28, wherein R.sup.31—R.sup.35 are independently selected from hydrogen, methyl, halogen and hydroxy, R.sup.41 is lower alkyl and Y.sup.4 is 0.
30. The compound of clause 1, having one of the formula (XLVIII) or formula (XLIX):
##STR00476##
wherein R.sup.1 is selected from aryl, substituted aryl, heteroaryl and substituted heteroaryl.
31. The compound of clause 30, wherein R.sup.4 is methyl, isopropyl, cyclohexyl, substituted cyclohexyl, phenyl, substituted phenyl, benzyl, substituted benzyl or —CH.sub.2-4-tetrahydropyran.
32. The compound of clause 30 or 31, wherein R.sup.1 is phenyl, a substituted phenyl, a pyridyl or a substituted pyridyl.
33. The compound of any one of clauses 1-32, wherein the compound is selected from the compounds of Table 2, 4, 5 and 6, or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
34. The compound of any one of clauses 1-32, wherein the compound is selected from the compounds of Table 1, or a prodrug thereof, or a pharmaceutically acceptable salt thereof.
35. An anti-infective pharmaceutical composition comprising: the compound of any one of clauses 1-34; and a pharmaceutically acceptable excipient.
36. A method of inhibiting a PI4-kinase, the method comprising contacting a sample comprising the PI4-kinase with the compound of any one of clauses 1-32.
37. The method of clause 36, wherein the PI4-kinase is a PI4-III kinase.
38. The method of clause 37, wherein the PI4-III kinase is a PI4KIIIα- or PI4KIIIβ-kinase.
39. A method of treating a subject for an infective disease condition, the method comprising administering to the subject a pharmaceutical composition comprising an effective amount of the compound of any one of clauses 1-33 or the pharmaceutical composition of clause 33, or a pharmaceutically acceptable salt thereof.
40. The method of clause 39, wherein the infective disease condition is caused by infection of a pathogen susceptible to PI4-kinase inhibition.
41. The method of clause 39, wherein the infective disease condition results from infection with a virus selected from the Picornaviridae, Flaviviridae, Caliciviridae, Filoviridae, Hepeviridae and Coronavirinae families.
42. The method of clause 39, wherein the infective disease condition results from infection with a pathogen selected from HCV, rhinovirus (e.g., A, B or C, as well as unclassified), P. falciparum, ebola virus, Francisella tularensis, hantavirus, SARS virus, MERS virus, vaccinia, smallpox, Japanese encephalitis virus, hepatitis A virus, and influenza virus, Norovirus, PolioVirus, Enterovirus (e.g., A-D), HEV, EV71, EV68, West Nile Virus, cytomegalovirus, P. aeruginosa, and Dengue Virus (e.g., 1-4).
43. The method of clause 42, wherein the pathogen is selected from EV71, EV68, human rhinoviruses, hepatitis A virus (e.g. HAV), HCV, norovirus and ebola virus.
44. The method of clause 42, wherein the pathogen is HCV.
45. The method of clause 42, wherein the pathogen is HAV.
46. The method of clause 42, wherein the pathogen is EV71 or EV68.
47. The method of clause 42, wherein the pathogen is a human rhinovirus.
48. The method of clause 42, wherein the pathogen is a norovirus.
49. The method of clause 42, wherein the pathogen is ebola virus.
50. The method of any one of clauses 41-49, wherein the compound is one of the compounds of Table 1 or Table 2.
51. The method of clause 41, wherein the compound has activity against two or more pathogens.