WO2005016000A1 - Derivatives of cyclic quinone and uses thereof - Google Patents

Derivatives of cyclic quinone and uses thereof

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Publication number
WO2005016000A1
WO2005016000A1 PCT/US2004/025038 US2004025038W WO2005016000A1 WO 2005016000 A1 WO2005016000 A1 WO 2005016000A1 US 2004025038 W US2004025038 W US 2004025038W WO 2005016000 A1 WO2005016000 A1 WO 2005016000A1
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invention
compound
gene
compounds
alkyl
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PCT/US2004/025038
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French (fr)
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Janak K. Padia
Sean O'brien
Jiemin Lu
Stanislaw Pikul
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Avalon Pharmaceuticals
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    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D241/00Heterocyclic compounds containing 1,4-diazine or hydrogenated 1,4-diazine rings
    • C07D241/36Heterocyclic compounds containing 1,4-diazine or hydrogenated 1,4-diazine rings condensed with carbocyclic rings or ring systems
    • C07D241/38Heterocyclic compounds containing 1,4-diazine or hydrogenated 1,4-diazine rings condensed with carbocyclic rings or ring systems with only hydrogen or carbon atoms directly attached to the ring nitrogen atoms
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D401/00Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/02Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
    • C07D401/06Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings linked by a carbon chain containing only aliphatic carbon atoms
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D403/00Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
    • C07D403/02Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
    • C07D403/06Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings linked by a carbon chain containing only aliphatic carbon atoms
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D471/00Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
    • C07D471/02Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
    • C07D471/04Ortho-condensed systems
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D487/00Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by C07D451/00 - C07D477/00
    • C07D487/02Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
    • C07D487/04Ortho-condensed systems
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D495/00Heterocyclic compounds containing in the condensed system at least one hetero ring having sulfur atoms as the only ring hetero atoms
    • C07D495/02Heterocyclic compounds containing in the condensed system at least one hetero ring having sulfur atoms as the only ring hetero atoms in which the condensed system contains two hetero rings
    • C07D495/04Ortho-condensed systems

Abstract

Chemical agents, such as derivatives of quinone, and including salts thereof, that modulate levels of gene expression in cellular systems, including cancer cells, are disclosed, along with methods for preparing such agents, as well as pharmaceutical compositions containing such agents as active ingredients and methods of using these as therapeutic agents.

Description

DERIVATIVES OF CYCLIC QUINONE AND USES THEREOF

This application claims priority of U.S. Provisional Application Serial No. 60/492,653, filed 5 August 2003, the disclosure of which is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to chemical agents affecting levels of gene expression in cellular systems, including cancer cells. In particular, the present invention relates to derivatives of quinone moiety, processes for their preparation, their use as antitumor drugs and pharmaceutical compositions containing them as active ingredients.

BACKGROUND OF THE INVENTION

Screening assays for novel drugs are based on the response of model cell based systems in vitro to treatment with specific compounds. Various measures of cellular response have been utilized, including the release of cytokines, alterations in cell surface markers, activation of specific enzymes, as well as alterations in ion flux and/or pH. Some such screens rely on specific genes, such as oncogenes or tumor suppressors. The present invention utilizes screening of small molecule compounds as potential anticancer drugs by taking advantage of the concept that for each specific tumor type, a unique signature set of genes, that are differentially expressed in tumor cells if compared to corresponding normal cells, can be established. The relatively small signature set, containing 10-30 genes, allows for easy, high throughput screening for compounds that can reverse the gene expression profile from patterns typical for cancer cells to patterns seen in normal cells. As a part of our efforts to provide new diversified compounds for high throughput gene expression screening, we designed and synthesized a number of novel derivatives of quinines. Gene expression screening and subsequent cytotoxicity screening revealed that some of the compounds possess biological activity. Consequently, detailed structure-activity relationship resulted in compounds of formula I as new small molecule agents having antineoplastic activity.

BRIEF SUMMARY OF THE INVENTION In one aspect, the present invention relates to organic compounds, derivatives of quinone, that have the ability to function as gene expression modulators for genes found in cancer cells, especially genes involved in misregulated signal transduction pathways typical for colon cancer. In one embodiment of the present invention, the compounds disclosed herein are able to up regulate genes found to be up regulated in normal (i.e., non-cancerous) cells versus cancer cells, especially colon cancer cells, thereby producing an expression profile for said gene(s) that resembles the expression profile found in normal cells. In another embodiment, the compounds disclosed herein are found to down regulate genes otherwise up- regulated in cancer cells, especially colon cancer cells, relative to normal (i.e., non-cancerous) cells thereby producing an expression profile for said gene(s) that more resembles the expression profile found in normal cells. Thus, in addition to activity in modulating a particular gene that may or may not have a major role in inducing or sustaining a cancerous condition, the agents disclosed herein also find value in regulating a set of gene whose combined activity is related to a disease condition, such as cancer, especially colon cancer, including adenocarcinoma of the colon. Thus, while an overall set of genes is modulated, the effect of modulating any subset of these may be disproportionately large or small with respect to the effect in ameliorating the overall disease process. Consequently, different disease conditions may rely on different subsets of genes to be active or inactive as a basis for the overall disease process.

Thus, the present invention relates to novel organic compounds that have the ability to function as gene modulators for genes found in normal (i.e., non-cancer) cells and which genes are found to be up regulated or down regulated in normal cells, especially colon cells. Such an effect may prevent a disease condition, such as cancer, from arising in those otherwise more susceptible to such a condition. In one such embodiment, administration of one or more of the agents disclosed herein may succeed in preventing a cancerous condition from arising.

In other embodiments, the agents disclosed herein find use in combination with each other as well as with other agents, such as where a mixture of one or more of the agents of the present invention are given in combination or where one or more of the agents disclosed herein is given together with some other already known therapeutic agent, possibly as a means of potentiating the affects of such known therapeutic agent or vice versa. The present invention also relates to processes of preventing or treating disease conditions, especially cancer, most especially colon cancer, by administering to a subject, such as a mammal, especially a human, a therapeutically active amount of one or more of the agents disclosed herein, including where such agents are given in combination with one or more known therapeutic agents.

DEFINITIONS

The following is a list of definitions for terms used herein. "Acyl" or "carbonyl" is a radical formed by removal of the hydroxy from a carboxylic acid (i.e., R-C(=O)-). Preferred acyl groups include (for example) acetyl, formyl, and propionyl.

"Alkyl" is a saturated hydrocarbon chain having 1 to 15 carbon atoms, preferably 1 to 10, more preferably 1 to 4 carbon atoms. "Alkene" is a hydrocarbon chain having at least one (preferably only one) carbon-carbon double bond and having 2 to 15 carbon atoms, preferably 2 to 10, more preferably 2 to 4 carbon atoms. "Alkyne" is a hydrocarbon chain having at least one (preferably only one) carbon-carbon triple bond and having 2 to 15 carbon atoms, preferably 2 to 10, more preferably 2 to 4 carbon atoms. Alkyl, alkene and alkyne chains (referred to collectively as "hydrocarbon chains") may be straight or branched and may be unsubstituted or substituted. Preferred branched alkyl, alkene and alkyne chains have one or two branches, preferably one branch. Preferred chains are alkyl. Alkyl, alkene and alkyne hydrocarbon chains each may be unsubstituted or substituted with from 1 to 4 substituents; when substituted, preferred chains are mono-, di-, or tri-substituted. Alkyl, alkene and alkyne hydrocarbon chains each may be substituted with halo, hydroxy, aryloxy (e.g., phenoxy), heteroaryloxy, acyloxy (e.g., acetoxy), carboxy, aryl (e.g., phenyl), heteroaryl, cycloalkyl, heterocycloalkyl, spirocycle, amino, amido, acylamino, keto, thioketo, cyano, or any combination thereof. Preferred hydrocarbon groups include methyl, ethyl, propyl, isopropyl, butyl, vinyl, allyl, butenyl, and exomethylenyl. Also, as referred to herein, a "lower" alkyl, alkene or alkyne moiety (e.g., "lower alkyl") is a chain comprised of 1 to 6, preferably from 1 to 4, carbon atoms in the case of alkyl and 2 to 6, preferably 2 to 4, carbon atoms in the case of alkene and alkyne.

"Alkoxy" is an oxygen radical having a hydrocarbon chain substituent, where the hydrocarbon chain is an alkyl or alkenyl (i.e., -O-alkyl or -O- alkenyl). Preferred alkoxy groups include (for example) methoxy, ethoxy, propoxy and allyloxy.

"Aryl" is an aromatic hydrocarbon ring. Aryl rings are monocyclic or fused bicyclic ring systems. Monocyclic aryl rings contain 6 carbon atoms in the ring. Monocyclic aryl rings are also referred to as phenyl rings. Bicyclic aryl rings contain from 8 to 17 carbon atoms, preferably 9 to 12 carbon atoms, in the ring. Bicyclic aryl rings include ring systems wherein one ring is aryl and the other ring is aryl, cycloalkyl, or heterocycloakyl. Preferred bicyclic aryl rings comprise 5-, 6- or 7-membered rings fused to 5-, 6-, or 7- membered rings. Aryl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring. Aryl may be substituted with halo, cyano, nitro, hydroxy, carboxy, amino, acylamino, alkyl, heteroalkyl, haloalkyl, phenyl, aryloxy, alkoxy, heteroalkyloxy, carbamyl, haloalkyl, methylenedioxy, heteroaryloxy, or any combination thereof. Preferred aryl rings include naphthyl, tolyl, xylyl, and phenyl. The most preferred aryl ring radical is phenyl.

"Aryloxy" is an oxygen radical having an aryl substituent (i.e., -O-aryl). Preferred aryloxy groups include (for example) phenoxy, napthyloxy, methoxyphenoxy, and methylenedioxyphenoxy.

"Cycloalkyl" is a saturated or unsaturated hydrocarbon ring. Cycloalkyl rings are not aromatic. Cycloalkyl rings are monocyclic, or are fused, spiro, or bridged bicyclic ring systems. Monocyclic cycloalkyl rings contain from about 3 to about 9 carbon atoms, preferably from 3 to 7 carbon atoms, in the ring. Bicyclic cycloalkyl rings contain from 7 to 17 carbon atoms, preferably from 7 to 12 carbon atoms, in the ring. Preferred bicyclic cycloalkyl rings comprise 4-, 5-, 6- or 7-membered rings fused to 5-, 6-, or 7-membered rings. Cycloalkyl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring. Cycloalkyl may be substituted with halo, cyano, alkyl, heteroalkyl, haloalkyl, phenyl, keto, hydroxy, carboxy, amino, acylamino, aryloxy, heteroaryloxy, or any combination thereof. Preferred cycloalkyl rings include cyclopropyl, cyclopentyl, and cyclohexyl.

"Halo" or "halogen" is fluoro, chloro, bromo or iodo. Preferred halo are fluoro, chloro and bromo; more preferred typically are chloro and fluoro, especially fluoro.

"Haloalkyl" is a straight, branched, or cyclic hydrocarbon substituted with one or more halo substituents. Preferred are C1-C12 haloalkyls; more preferred are C-i-Cβ haloalkyls; still more preferred still are C1-C3 haloalkyls.

Preferred halo substituents are fluoro and chloro. The most preferred haloalkyl is trifluoromethyl.

"Heteroatom" is a nitrogen, sulfur, or oxygen atom. Groups containing more than one heteroatom may contain different heteroatoms. "Heteroalkyl" is a saturated or unsaturated chain containing carbon and at least one heteroatom, wherein no two heteroatoms are adjacent. Heteroalkyl chains contain from 2 to 15 member atoms (carbon and heteroatoms) in the chain, preferably 2 to 10, more preferably 2 to 5. For example, alkoxy (i.e., -O-alkyl or -O-heteroalkyl) radicals are included in heteroalkyl. Heteroalkyl chains may be straight or branched. Preferred branched heteroalkyl have one or two branches, preferably one branch. Preferred heteroalkyl are saturated. Unsaturated heteroalkyl have one or more carbon-carbon double bonds and/or one or more carbon-carbon triple bonds. Preferred unsaturated heteroalkyls have one or two double bonds or one triple bond, more preferably one double bond. Heteroalkyl chains may be unsubstituted or substituted with from 1 to 4 substituents. Preferred substituted heteroalkyl are mono-, di-, or tri-substituted. Heteroalkyl may be substituted with lower alkyl, haloalkyl, halo, hydroxy, aryloxy, heteroaryloxy, acyloxy, carboxy, monocyclic aryl, heteroaryl, cycloalkyl, heterocycloalkyl, spirocycle, amino, acylamino, amido, keto, thioketo, cyano, or any combination thereof.

"Heteroaryl" is an aromatic ring containing carbon atoms and from 1 to about 6 heteroatoms in the ring. Heteroaryl rings are monocyclic or fused bicyclic ring systems. Monocyclic heteroaryl rings contain from about 5 to about 9 member atoms (carbon and heteroatoms), preferably 5 or 6 member atoms, in the ring. Bicyclic heteroaryl rings contain from 8 to 17 member atoms, preferably 8 to 12 member atoms, in the ring. Bicyclic heteroaryl rings include ring systems wherein one ring is heteroaryl and the other ring is aryl, heteroaryl, cycloalkyl, or heterocycloalkyl. Preferred bicyclic heteroaryl ring systems comprise 5-, 6- or 7-membered rings fused to 5-, 6-, or 7-membered rings. Heteroaryl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring. Heteroaryl may be substituted with halo, cyano, nitro, hydroxy, carboxy, amino, acylamino, alkyl, heteroalkyl, haloalkyl, phenyl, alkoxy, aryloxy, heteroaryloxy, or any combination thereof. Preferred heteroaryl rings include, but are not limited to, the following:

Furan Thiophene Pyrrole Pyrazole Imidazole Oxazole Isoxazole Isothiazole Thiazole 1 ,2,5-Thiadiazole 1 ,2,3-Triazole 1 ,3,4-Thiadiazole Furazan 1 ,2,3-T iadiazole 1 ,2,4-T iadiazole Benzotriazole 1 ,2,4-Triazole Tetrazole

1,2,4-Oxadiazole 1 ,3,4-Oxadiazole 1 ,2,3,4-Oxatriazole 1 ,2,3,4-Thiatriazole 1 ,2,3,5-T iatriazole

1,2,3, Pyridine Pyridazine Pyrimidine Pyrazine 1 ,3,5-Triazine lndolizine

Isoindole Benzofuran Benzothiophene "I H-lndazole Purine Quinoline

B oenzimtidjazole B αenzthia>zole Benzoxazole Pteridine c

Isoquinoline Cinnoline Phthalazine Quinazoline Quinoxaline 1,8-Napthypyridine

Phenazine "Heteroaryloxy" is an oxygen radical having a heteroaryl substituent

(i.e., -O-heteroaryl). Preferred heteroaryloxy groups include (for example) pyridyloxy, furanyloxy, (thiophene)oxy, (oxazole)oxy, (thiazole)oxy, (isoxazole)oxy, pyrmidinyloxy, pyrazinyloxy, and benzothiazolyloxy. "Heterocycloalkyl" is a saturated or unsaturated ring containing carbon atoms and from 1 to about 4 (preferably 1 to 3) heteroatoms in the ring. Heterocycloalkyl rings are not aromatic. Heterocycloalkyl rings are monocyclic, or are fused, bridged, or spiro bicyclic ring systems. Monocyclic heterocycloalkyl rings contain from about 3 to about 9 member atoms (carbon and heteroatoms), preferably from 5 to 7 member atoms, in the ring. Bicyclic heterocycloalkyl rings contain from 7 to 17 member atoms, preferably 7 to 12 member atoms, in the ring. Bicyclic heterocycloalkyl rings contain from about 7 to about 17 ring atoms, preferably from 7 to 12 ring atoms. Bicyclic heterocycloalkyl rings may be fused, spiro, or bridged ring systems. Preferred bicyclic heterocycloalkyl rings comprise 5-, 6- or 7- membered rings fused to 5-, 6-, or 7-membered rings. Heterocycloalkyl rings may be unsubstituted or substituted with from 1 to 4 substituents on the ring. Heterocycloalkyl may be substituted with halo, cyano, hydroxy, carboxy, keto, thioketo, amino, acylamino, acyl, amido, alkyl, heteroalkyl, haloalkyl, phenyl, alkoxy, aryloxy or any combination thereof. Preferred substituents on heterocycloalkyl include halo and haloalkyl. Preferred heterocycloalkyl rings include, but are not limited to, the following: Oxirane Aziridine Oxetane Azetidine Tetrahydrofuran Pyrrolidine 3H-lndole 1 ,3-Dioxolane 1,2-Dithiolane 1,3-Dithiolane 4,5-Dihydroisoxazole 2,3-Dihydroisoxazole

P ύyrazo-lidine 2H O-Pyran 3,4-Dih 0ydro-2H-pyran Tetra Ohydropyran 2 C/-/-COromene

Chromone Chroman Piperidine Morpholine 4/-/-1 ,3-Oxazine 6H-1 ,3-Oxazine

5,6-dihydro 0-4W-1°,3-oxazine 4H c-3,1-be?nzoxazine 1,3-Dioxane

Cepham Piperazine Hexa 6hydroazepine 1, O3-Dithiane 1,40-Dioxane Penem

outnarin Thiomorp oline Thymine Th ciolane

2,3-Dihydro-1H-lsoindole Phthalan 1,4-Oxat iane 1,4-Dithiaπe hexahydro-Pyridazine

1 ,2-Benzisothiazoline Benzylsultam

While alkyl, heteroalkyl, cycloalkyl, and heterocycloalkyl groups may be substituted with hydroxy, amino, and amido groups as stated above, the following are not envisioned in the invention: Enols (OH attached to a carbon bearing a double bond).

Amino groups attached to a carbon bearing a double bond (except for vinylogous amides).

More than one hydroxy, amino, or amido attached to a single carbon (except where two nitrogen atoms are attached to a single carbon atom and all three atoms are member atoms within a heterocycloalkyl ring).

Hydroxy, amino, or amido attached to a carbon that also has a heteroatom attached to it.

Hydroxy, amino, or amido attached to a carbon that also has a halogen attached to it. A "pharmaceutically-acceptable salt" is a cationic salt formed at any acidic (e.g., carboxylic acid) group, or an anionic salt formed at any basic (e.g., amino) group. Many such salts are known in the art, as described in World Patent Publication 87/05297, Johnston et al., published September 11, 1987 incorporated by reference herein. Preferred cationic salts include the alkali metal salts (such as sodium and potassium), and alkaline earth metal salts (such as magnesium and calcium) and organic salts. Preferred anionic salts include the halides (such as chloride salts), sulfonates, carboxylates, phosphates, and the like.

Such salts are well understood by the skilled artisan, and the skilled artisan is able to prepare any number of salts given the knowledge in the art. Furthermore, it is recognized that the skilled artisan may prefer one salt over another for reasons of solubility, stability, formulation ease and the like. Determination and optimization of such salts is within the purview of the skilled artisan's practice.

A "solvate" is a complex formed by the combination of a solute (e.g., a metalloprotease inhibitor) and a solvent (e.g., water). See J. Honig et al., The Van Nostrand Chemist's Dictionary, p. 650 (1953). Pharmaceutically-acceptable solvents used according to this invention include those that do not interfere with the biological activity of the metalloprotease inhibitor (e.g., water, ethanol, acetic acid, N,N- dimethylformamide and others known or readily determined by the skilled artisan).

The terms "optical isomer", "stereoisomer", and "diastereomer" have the accepted meanings (see, e.g., Hawlev's Condensed Chemical Dictionary. 11th Ed.). The illustration of specific protected forms and other derivatives of the compounds of the instant invention is not intended to be limiting. The application of other useful protecting groups, salt forms, etc. is within the ability of the skilled artisan.

DETAILED SUMMARY OF THE INVENTION

In one aspect, the present invention relates to a compound having the structure of Formula (I)

wherein W, X, Y and Z are each independently selected from a bond (meaning that said group or substituent is not present), C-R4, C-R5, C-R6 C-R7, O (oxygen), N (nitrogen) or S (sulfur) and that no more than two W, X, Y and Z are O, N and S; wherein, R4, R5, R6, and R7 each independently hydrogen, hydroxyl, sulfhydryl, alkoxy, thioalkoxy, alkyl, halogen, CN, CF3, NO2, COORβ, CONR8R9, NR8R9, NR8COR9, NR8SO2R9, NR8CONR90; wherein R8, R9 and Rio are independently hydrogen, alkyl, heteroalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyl, and heterocycloalkyl; NR8Rg is also unsubstituted, monosubstituted or polysubstituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; H alkyl, unsubstituted, mono or polysubstituted phenyl or polyaromatic, unsubstituted, mono or polysubstituted heteroaromatic, with hetero atom(s) as N, O, S, Unsubstituted, mono or polysubstituted aralkyl,

Unsubstituted, mono or polysubstituted cyclo or polycyclo hydrocarbon or mono or polyheterocycle (3-8 atoms per ring) with one to four hetero atoms as N, O, or S ; and wherein substitutions are independently selected from hydrogen, hydroxyl, sulfhydryl, alkoxy, thioalkoxy, alkyl, halogen, CN, CF3, NO2, COOR8, CONR8R9, NR8R9, NR8COR9, NR8SO2R9, NRι0CONR8R9 wherein R8, R9 and R10 are independently as mentioned above; NR8R9 is also unsubstituted, monosubstituted or polysubstituted mono or polycyclic ring with one to four heteroatoms such as N, O, S; Additionally, R8 and Rio can be connected together to form 4, 5,6 or 7-member cyclic ring system;

Ri and R3 are also independently selected from:

wherein n is 2, 3, 4 and Rn, R12, R13 and Rι4 are independently selected from hydrogen, alkyl, cycloalkyl, unsubstituted or substituted aryl, unsubstituted or substituted heteroaryl, unsubstituted or substituted alkylaryl; NR13R14 is also unsubstituted, or substituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; Additionally, Rn and R13 can be connected together to form 4, 5,6 or 7-member cyclic ring system; R2 is also selected from:

- -NRi3CONR14R15 ;

- >

-CONR13R.|, wherein n is 0, 1, 2 and 3 and Rn, R12, R13 and R14 are independently selected from hydrogen, alkyl, unsubstituted or substituted cycloalkyl, unsubstituted or substituted aryl, unsubstituted or substituted alkaryl ; NR-13R14 is also unsubstituted or substituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; additionally, Rn and R13 can be connected together to form 4, 5, 6 or 7 member ring system provided n is 1, 2, and 3; including salts thereof. In a preferred embodiment of such compounds, the present invention includes compounds of Formula I wherein: W, X, Y and Z are each independently selected from a bond, C-R4, C- R5, C-R6 C-R7, O (oxygen), N (nitrogen) or S (sulfur) and that no more than two of W, X, Y and Z are O, N and S; wherein, R4, R5, R6, and R7 each independently hydrogen, hydroxyl, sulfhydryl, lower alkoxy, (1-6 carbon atoms), lower thioalkoxy (1-6 carbon atoms), alkyl, halogen, CN, CF3, NO2, COOR8, CONR8R9, NR8R9, NR8COR9, NR8S02R9, NR8CONR9Rιo; wherein R8, R9 and R10 are independently hydrogen, alkyl, H, alkyl, heteroalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyl, and heterocycloalkyl; NR8Rg is also mono or bicyclic ring, with one to four heteroatoms such as N, O, S; Rι, R2 and R3 are: H alkyl of 1 to 6 carbon atoms, unsubstituted, mono or polysubstituted phenyl or polyaromatic, unsubstituted, mono or polysubstituted heteroaromatic, with hetero atom(s) as N, O, S, Unsubstituted, mono or polysubstituted aralkyl, Unsubstituted, mono or polysubstituted cyclo or polycyclo hydrocarbon or mono or polyheterocycle (3-8 atoms per ring) with one to four hetero atoms as N, O, or S ; and wherein substitutions are selected from independently hydrogen, hydroxyl, sulfhydryl, lower alkoxy, (1-6 carbon atoms), lower thioalkoxy (1-6 carbon atoms), alkyl, halogen, CN, CF3, NO2, COOR8, CONR8Rg, NR8R9, NR8CORg, NR8SO2Rg, NRι0CONR8R9 wherein R8, R9 and R10 are independently as mentioned above; NR8Rg is also mono or polycyclic ring with one to four heteroatoms such as N, O, S; additionally, R8 and Rio can be connected together to form 4, 5,6 or 7- member cyclic ring system;

Ri and R3 are also independently selected from:

-NR13C0NR1 R15 ;

wherein n is 2, 3, 4, 5, 6 and R11 ( R12, R13 and R14 are independently selected from hydrogen, alkyl, cycloalkyl, aryl, heteroaryl, alkylaryl from 7 to 10 carbon atoms; NR13R14 is also mono or bicyclic ring with one to four heteroatoms such as N, O, S; Additionally, Rn and R13 can be connected together to form 4, 5,6 or 7-member cyclic ring system;

R2 is also selected from:

wherein n is 0, 1, 2 , 3, 4, 5 and Rn, R12, R13 and R14 are independently selected from hydrogen, alkyl, cycloalkyl, aryl, alkaryl from 7 to 10 carbon atoms; NR13R14 is also mono or bicyclic ring with one to four heteroatoms such as N, O, S; additionally, Rn and R13 can be connected together to form 4, 5,6 or 7 member ring system provided n is 1 , 2, and 3; including salts thereof.

In a preferred embodiment of the latter compounds, W and Z are each independently C-R4, C-R7 or N while X and Y are each independently C-R5 or C-R6. In a highly preferred embodiment of the latter, W is C-R4 or N and X, Y and Z are each independently C-R5, C-Rβ or C-R . In another such highly preferred embodiment, Z is C-R , C-R5, C-R or N and W and Y are each independently C-R4, C-R6 or C-R7.

In another preferred embodiment, the compounds of the present invention include compounds of Formula I wherein X and Y are each independently C-R5, C-R6 or N and wherein W and Z are each independently C-R4 or C-R5. In a most preferred embodiment of the latter compounds, X is C-R5 or N and W, Y and Z are each independently C-R4, C-R6 or C-R7. In another such embodiment, Y is C-R4, C-R5, C-R6, C-R7 or N and X and Z are each independently C-R4, C-R5 or C-R7. Especially preferred in the latter group are compounds wherein W X, Y and Z are each independently C-R4, C- R5, C-RQ or C-R7. In a highly preferred embodiment of the latter, the compound has the general structure:

most preferably wherein Ri and R3 are selected from -hydrogen, -alkyl, cycloalkyl, unsubstituted or substituted phenyl, unsubstituted or substituted benzyl, -methylpyridine, -ethylpyridine, -mehtylindole, -ethylindole, alkoxyethyl-, hydroxyethyl, N,N-dialkyl-ehtyl, , N,N-dialkyl-propyl, methylpyrrole, ethylpyrrole, methylfuran, ethylfuran, -alkyimorpholine, - alkylpiperizine, -alkypiperidine, -alkylpyrrolidine, and R2 is H or lower alkyl.

In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein R1 is

wherein n is 2, 3 and 4 and R2 is H or lower alkyl. In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein R is wherein n is 2, 3 and 4 and R2 is H or lower alkyl.

In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein Ri is

wherein n is 2, 3 and 4 and R2 is H or lower alkyl.

In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein R3 is

wherein n is 2, 3 and 4 and R2 is H or lower alkyl.

In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein R1 is

wherein n is 2, 3 and 4 and R2 is H or lower alkyl.

In another highly preferred embodiment of this structure, the compounds of the invention have structures wherein R3 is

R11

-NR13S024

R12 wherein n is 2, 3 and 4 and R is H or lower alkyl.

In additional highly preferred embodiments, the compounds of the invention have the structure of Formula I wherein Ri is

wherein n is 2, 3 and 4 and R2 is H or lower alkyl. In another highly preferred embodiment, the compounds of the invention have the structure of Formula I wherein R3 is

wherein n is 2, 3 and 4 and R2 is H or lower alkyl.

In another highly preferred embodiment, the compounds of the invention have the structure of Formula I wherein Ri is wherein n is 2, 3 and 4 and R2 is H or lower alkyl.

In another highly preferred embodiment, the compounds of the invention have the structure of Formula I wherein R3 is

wherein n is 2, 3 and 4 and R2 is H or lower alkyl.

In another highly preferred embodiment, the compounds of the invention have the structure of Formula I wherein Ri is

wherein n is 2, 3 and 4 and R2 is H or lower alkyl.

In another highly preferred embodiment, the compounds of the invention have the structure of Formula I wherein R3 is

R 11

-NR13S024

R12 wherein n is 2, 3 and 4 and R2 is H or lower alkyl.

In highly preferred embodiments, the present invention encompasses compounds having a structure found in Table 1, 2, 3, 4, 5, 6. 7, 8, 9, 10, 11, 12, or 13 including salts of any of these, preferably pharmaceutically acceptable salts thereof.

In another aspect, the present invention relates to compositions of any of the compounds of the invention, preferably wherein such compound is present in a pharmaceutically acceptable carrier and in a therapeutically effective amount. Such compositions will generally comprise an amount of such compound that is not toxic (i.e., an amount that is safe for therapeutic uses). In accordance with the foregoing, the present invention is directed to use of the compounds of the invention as active ingredients for medicaments, in particular for medicaments useful for the treatment of tumors. The compounds of the invention will thus be present in pharmaceutical compositions containing compounds of formula I as active ingredients, in admixture with pharmaceutically acceptable vehicles and excipients, which includes any pharmaceutical agent that does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity. Pharmaceutically acceptable carriers include, but are not limited to, liquids such as water, saline, glycerol and ethanol, and the like, including carriers useful in forming sprays for nasal and other respiratory tract delivery or for delivery to the ophthalmic system. A thorough discussion of pharmaceutically acceptable carriers, diluents, and other excipients is presented in REMINGTON'S PHARMACEUTICAL SCIENCES (Mack Pub. Co., N.J. current edition). Use of such carriers is well known to those skilled in the art and will not be discussed further herein. Also in accordance with the foregoing, the present invention relates to a method for preventing or treating a disease associated with a change in levels of expression of particular sets of genes in a mammal comprising administering to said mammal an effective amount of a compound of the invention.

In another aspect, the present invention relates to a method for preventing or treating a disorder modulated by altered gene expression, wherein the disorder is selected from the group consisting of cancer, cardiovascular disorders, arthritis, osteoporosis, inflammation, periodontal disease and skin disorders, comprising administering to a mammal in need of such treatment or prevention a therapeutically effective amount of a compound of the invention. In a preferred embodiment thereof, the disorder is cancer, more preferably colon cancer, most preferably adenocarcinoma, and the treatment prevents, arrests or reverts tumor growth, metastasis or both.

The compounds of the invention will commonly exert a therapeutic effect by modulation of one or more genes found in a cell, especially a mammalian cell, such as a cancer cell, preferably colon cancer and most preferably adenocarcinoma. Thus, a compound, or compounds, of the invention can be used to determine or demarcate a set of genes by determining modulation of such set of genes by one or more compounds of the invention. For example, where a set of genes is found to be up-regulated in cancer cells versus otherwise normal cells, especially normal cells of the same tissue or organ as the cancer cells, a set of genes can be determined by their common property of being modulated (based on a change in expression of the genes, such as a change in rate or amount of RNA transcribed or the amount of polypeptide produced by said expression) by contacting such genes, or a cell containing such genes, with one or more of the compounds of the invention. The extent of such modulation may, of course, be related to the amount of said compound, or compounds, used in the contacting. Such modulation may include the increased expression of all the determined genes (i.e., the genes of the set), the decreased expression of all genes of the set, or the increase in expression of some of the genes of the set and decreased expression of others. Thus, a gene not modulated by the test compound (the compound used in contacting the genes or cell containing them) is not considered a member of the set.

Thus, the present invention relates to a gene set wherein expression of each member of said gene set is modulated as a result of contacting said gene set with a compound of the invention. In specific embodiments, expression of each member of said gene set is increased as a result of said contacting or is decreased as a result of said contacting. In another preferred embodiment, the gene set is present in a cell. Such a gene set will commonly be related to a specific disease process, such as a set of genes all of which are modulated by a compound of the invention wherein such compound has a specific therapeutic effect, such as being an anti-neoplastic agent.

In another aspect, the present invention relates to a method for identifying an agent that modulates the expression of a gene set of the invention, comprising: (a) contacting, or otherwise using, a compound, such as a test compound, a test system, such as a source of genes or polynucleotides, for example, those found to be related to a given disease or disorder, or a set that is modulated by a given compound, or group of compounds, especially where these are found in a cell, so that the cell represents the test system, containing one or more polynucleotides corresponding to each of the members of the gene set of the invention under conditions wherein the members of said gene set are being expressed; (b) determining a change in expression of each of said one or more polynucleotides of step (a) as a result of said treatment; wherein said change in expression of step (b) indicates modulation of the members of said gene set by the test compound thereby identifying a test compound that modulates the expression of said gene set. In one embodiment, the cell is a naturally derived cell that contains genes of a gene set or may be a recombinant cell engineered to comprise the genes or polynucleotides of the gene set. In an alternative embodiment, the test system may comprise the genes or polynucleotides in a cell-free system. In a related aspect, the present invention provides a method for identifying a test compound that modulates the expression of a gene set, such as a gene set of the invention, comprising: (a) contacting a test compound with one or more polynucleotides corresponding to each of the members of the gene set of the invention under conditions wherein the members of said gene set are being expressed; (b) determining a change in expression of each of said one or more polynucleotides of step (a) as a result of said contacting; wherein said change in expression of step (b) indicates modulation of the members of said gene set thereby identifying a test compound that modulates the expression of said gene set.

As used herein, "corresponding genes" or "corresponding polynucleotides" or "polynucleotides corresponding to genes" refers to polynucleotides and/or genes that encode an RNA that is at least 90% identical, preferably at least 95% identical, most preferably at least 98% identical, and especially identical, to an RNA encoded by one of the genes disclosed herein in Tables 8 and 9. Such genes will also encode the same polypeptide sequence, but may include differences in such amino acid sequences where such differences are limited to conservative amino acid substitutions, such as where the same overall three dimensional structure, is maintained. A "corresponding gene" includes splice variants thereof. Because a polynucleotide or gene used in the methods of the invention "corresponds to" a gene present in one of the gene sets of the invention, such as genes identified in Tables 8 and 9, such polynucleotide or gene encodes an RNA (processed or unprocessed, including naturally occurring splice variants and alleles) that is at least 90% identical, preferably at least 95% identical, most preferably at least 98% identical to, and especially identical to, an RNA that would be encoded by, or be complementary to, such as by hybridization with, a gene of Table 14 or 15, or genes of any gene set identified according to the invention. Polynucleotides encoding the same proteins as any of these genes, regardless of the percent identity of the sequences of such genes and/or polynucleotides, are also specifically contemplated by any of the methods of the present invention. The polynucleotides used in the methods of the invention also include any open reading frames, as defined herein, present therein. As used herein, the term "open reading frame" (or ORF) means a series of triplets coding for amino acids without any termination codons and is a sequence (potentially) translatable into protein.

The polynucleotides useful in the methods of the invention may be genomic in nature and thus represent the sequence of an actual gene, such as a human gene, or may be a cDNA sequence derived from a messenger

RNA (mRNA) and thus represent contiguous exonic sequences derived from a corresponding genomic sequence, or they may be wholly synthetic in origin for purposes of practicing the processes of the invention. Because of the processing that may take place in transforming the initial RNA transcript into the final mRNA, the sequences disclosed herein may represent less than the full genomic sequence. They may also represent sequences derived from ribosomal and transfer RNAs. Consequently, the gene as present in the cell

(and representing the genomic sequence) and the polynucleotide transcripts disclosed herein, including cDNA sequences, may be identical or may be such that the cDNAs contain less than the full genomic sequence. Such genes and cDNA sequences are still considered "corresponding sequences" (as defined elsewhere herein) because they both encode the same or related RNA sequences (i.e., related in the sense of being splice variants or RNAs at different stages of processing). Thus, by way of non-limiting example only, a gene that encodes an RNA transcript, which is then processed into a shorter mRNA, is deemed to encode both such RNAs and therefore encodes an RNA complementary to (using the usual Watson-Crick complementarity rules), or that would otherwise be encoded by, a cDNA (for example, a sequence as disclosed herein). Thus, the sequences disclosed herein correspond to genes contained in the cancerous cells (here, breast cancer) and are used to determine gene activity or expression because they represent the same sequence or are complementary to RNAs encoded by the gene. Such a gene also includes different alleles and splice variants that may occur in the cells used in the methods of the invention, such as where recombinant cells are used to assay for anti-neoplastic agents and such cells have been engineered to express a polynucleotide as disclosed herein, including cells that have been engineered to express such polynucleotides at a higher level than is found in non-engineered cancerous cells or where such recombinant cells express such polynucleotides only after having been engineered to do so. Such engineering includes genetic engineering, such as where one or more of the polynucleotides disclosed herein has been inserted into the genome of such cell or is present in a vector.

Such cells, especially mammalian cells, may also be engineered to express on their surfaces one or more of the polypeptides of the invention for testing with antibodies or other agents capable of masking such polypeptides and thereby removing the cancerous nature of the cell. Such engineering includes both genetic engineering, where the genetic complement of the cells is engineered to express the polypeptide, as well as non-genetic engineering, whereby the cell has been physically manipulated to incorporate a polypeptide of the invention in its plasma membrane, such as by direct insertion using chemical and/or other agents to achieve this result. In a preferred embodiment of such method, the determined change in expression is a decrease in expression of said one or more polynucleotides or a decrease in said expression. In other preferred embodiments, the determined change in expression is a change in transcription of said one or more polynucleotides or a change in activity of a polypeptide, or expression product, encoded by said polynucleotide, including a change in the amount of said polypeptide synthesized, such as by a cell. The term "expression product" means that polypeptide or protein that is the natural translation product of the gene and any nucleic acid sequence coding equivalents resulting from genetic code degeneracy and thus coding for the same amino acid(s).

In additional preferred embodiments, said one or more polynucleotides are present in a cell, preferably a cancer cell, more preferably a colon cancer cell, and most preferably where the colon cancer cell is an adenocarcinoma cancer cell. In another preferred embodiment of the invention, the cell is a recombinant cell engineered to contain said set of genes.

Such methods serve to identify other compounds that have like activity, including expected therapeutic activity, as the compounds of the invention and thus serve as the basis for large scale screening assays for therapeutic compounds. As a result, one or more compounds of the invention can be utilized to determine the presents of gene sets and subsets within the genome of a cell. Thus, the set of all genes modulated by a group of structurally related compounds of the invention can form a gene set while the different sets of genes regulated by each compound of a group will form a subset. By way of non-limiting example, where a structurally related group of 5 of the compounds of the invention (all having generally the structure of Formula I) modulate (by increasing or decreasing) expression of determined genes 1-20, this latter group of genes forms a gene set. Further examination then determines that genes 1-6 are modulated by compound A, genes 7-10 are modulated by compound B, genes 2-4 and 9-12 are modulated by compound C, genes 10-20 are modulated by compound D and the even numbered genes are modulated by compound E. Each of these groups of genes, such as the genes modulated by compound C, is considered a subset of the gene set of genes 1-20. In an analogous manner, the genes modulated by compound E can be themselves further subdivided into at least 2 subsets wherein one subset is made up of the genes whose expression is increased by compound E while the other subset is made up of genes whose expression is decreased by compound E, thus yielding subsets of subsets. It should be noted that within the context of the present invention, it is not necessary to identify subsets and that each so-called subset is, in its own right, a gene set as used in the invention. The identification of sets and subsets is thus a function of the extent that a user of the methods of the invention wishes to determine modulation of genes resulting from contacting of one or more compounds of the invention. Thus, the genes modulated by a single compound form a gene set and it is not necessary, in carrying out the methods of the invention, to compare different groups of genes for modulation by more than one compound but this may, of course, be done.

In accordance with the foregoing, the present invention relates to a set of genes comprising a plurality of subsets of genes wherein each subset of said plurality is a gene set identified by the methods of the invention. The present invention also relates to compounds identified as having activity using the methods of the invention, such as novel compounds not specifically described herein by structure but which have been identified by their ability to modulates one or more gene sets modulated by compounds of the invention.

In a preferred embodiment, the present invention encompasses the gene sets and subsets of the genes identified in Table 14 and/or in Table 15.

In using the compounds of the invention for treatment of disease, especially cancer, the present invention specifically contemplates use of a compound that modulates the expression of a set of, or subset of, genes of Table 15. The present invention also comprises methods for the preparation of compounds of formula I, and the relative key intermediates

Compound Preparation:

The compounds of the invention can be prepared using a variety of procedures known in the art. The starting materials used in preparing the compounds of the invention are known, made by known methods, or are commercially available. Particularly preferred syntheses are described in the following general reaction schemes.

Scheme 1 :

The dichloro compound 1 is either commercially available or can be synthesized using methods known in the literature. 1. Shaikh I. A. et al, J. Med. Chem, 29(8), 1329-1340, (1986) 2. Vlderrama el al, Syn. Comrn., 27(12), 2143-2157, (1997) 3. Chu, Kwong-Yung; et al. Journal of the Chemical Society, Perkin Transactions 1: Organic and Bio-Organic Chemistry (1972-1999) (1978) 4. Matsuhisa A. et al, Patent WO 01/60803 A1 The compound 1 can be reacted with an amine in an appropriate solvent to provide the corresponding derivative 2. The compound 2 then can be reacted with an apporopriate 2-halo, 2-substituted acetyl halide to obtain the corresponding 3 derivatives. A reaction of crude or purified compound 3 with an amine can give compound 4. Compound 4 with or without isolation can be treated with a organic or inorganic base in a suitable solvent at an appropriate temperature can provide desired compound 5 of formula I. Additionally, further independent modification each R1 ( R2 and R3 using methods known in literature to obtain additional compounds of formula I. Compounds for which no preparation is given can be made by methods known in the literature or are of common knowledge by skilled artisan.

The skilled artisan will recognize that some reactions are best carried out when another potentially reactive functionality on the molecule is masked or protected, thus avoiding any undesirable side reactions and/or increasing the yield of the reaction. Often protecting groups are used to accomplish such increased yields or to avoid the undesired reactions. Such reactions are well within the ability of the skilled artisan. Some examples are found in T. Greene, Protecting Groups in Organic Synthesis.

In addition, it is to be appreciated that one optical isomer may have favorable properties over the other and thus the disclosure of a racemic mixture within the present invention may also include either optically active isomer if such isomer has advantageous physiological activity in accordance with the methods of the invention.

Example-A1 2-Chloro-3-methylamino-f1,4lnaphthoguinone

To a solution of 22.7g (lOOmmol, 1 equivalent) of 2,3-dichloro-

[1 ,4]naphthoquinone in 350 ml of anhydrous THF was added 200ml of 2.0M methyl amine in THF (200mmol, 2 equivalents). To the mixture was added 34 ml of N, N-diisopropylethylamine (200mmol, 2 equivalents) and it was shaken at room temperature for overnight (16-20 hours).

The red precipitates formed were filtered and washed with ether. The residue was again washed with water and ether. The solid was dried under vacuum. The filtrate was checked for the desired product, and then THF was evaporated. The residue was recrystallized with DCM/ether. The titled compound was collected as a red solid (18g, Yield 74% ).

In a process analogous to Example A1 using appropriate starting materials, the corresponding compounds are prepared as follows:

Example-B1 2-Bromo-N-(3-chloro-1 ,4-dioxo-1.4-dihvdro-naphthalen-2-yl.- propionamide

To a solution of 2.08g of 2-amino-3-chloro-[1,4]naphthoquinone (10mmol, lequivalent) in 250 ml 1 ,4-dioxane was added 2.67g of K2CO3 (20mmol, 2equivalents). The mixture was heated until the starting material was completely dissolved. To the solution 4.2ml of 2-bromopropionylbromide (40mmol, 4 equivalents) was added and refluxed for 16 hours. Inorganic materials were filtered and washed thoroughly with DCM. The filtrate was evaporated and the residue recrystallized with DCM/ether or hexanes. The titled compound was collected as a light green solid (1.7g Yield, 50%).

In a process analogous to Example B1 using appropriate starting materials, the corresponding compounds are prepared as follows:

2-Bromo-N-(3-chloro-1,4-dioxo-1,4-dihydro-naphthalen-2-yl)-acetamide 2-Bromo-N-(3-chloro-1 ,4-dioxo-1 ,4-dihydro-naphthalen-2-yl)-N-methyl- acetamide

2-Bromo-N-(3-chloro-1,4-dioxo-1,4-dihydro-naphthalen-2-yl)-N-methyl- propionamide

Example-C1 2-Chloro-N-(3-chloro-1 ,4-dioxo-1 ,4-dihydro-naphthalen-2-yl)-N-methyl- acetamide

To a solution of 10g of 2-chloro-3-methylamino-[1,4]naphthoquinone (45 mmol) in 250 mL of dioxane was added 172 ml of chloroacetyl chloride (48 equivalents). The reaction was heated at 85° C for 16 hours. The solvent was evaporated and the material was purified on silica gel using dichloromethane and hexanes as solvents. The pure fractions were combined and the solvent was evaporated. The product was collected as a yellow/brown solid. (12.1g, Yield 90%).

In a process analogous to Example C1 using appropriate 2-chloro-3- substituted amino-[1,4 ]naphthoquinone (Example A) and corresponding acid chloride following compounds are prepared.

Example-D1

2-Chloro-N-(3-chloro-1 ,4-dioxo-1.4-dihvdro-naphthalen-2-vπ-N-methyl-

2- phenyl-acetamide

To a solution of 2 g of 2-chloro-3-methylamino-[1 ,4]naphthoquinone (9mmol, lequivalent) in 30 ml anhydrous 1 ,4-dioxane was added 20g(106mmol, 12equivalents) of 2-chloro-2-phenylacetyl chloride. The mixture was refluxed for 16 hours. The reaction mixture was concentrated and purified column chromatography on silica gel using gradient system from 100% hexanes to 100% ethyl acetate. Fractions containing the desired product peak were combined and evaporated. The residue was further purified by crystallization using ethyl acetate. The crystals were filtered and washed with ethyl acetate and then with hexanes. The titled compound was collected as a light yellow solid (2g, Yield 59%).

Example 1 (Compound 1, Table 1)

4-(2-Diethylamino-ethyl)-3-methyl-3,4-dihvdro-1 H-benzofglαuinoxaline-2,5.10- trione

To a solution of 100 mg of 2-bromo-N-(3-chloro-1 ,4-dioxo-1 ,4-dihydro- naphthalen-2-yl)-acetamide (0.28 mmol, 1 equivalent) in 10 ml of anhydrous THF was added 40 micro liters of N,N-diethylethylenediamine (0.28 mmol, 1 equivalent) in 1ml of THF. The amine solution was added in three portions over one hour. The mixture was heated at 60 °C for one hour. To the mixture, 20 mg of NaH (95%) (0.84mmol, 3 equivalents) was added in two portions waiting 15minutes after each addition. Then 0.5ml DMSO was added to the reaction and the mixture was stirred for one hour. Precipitates were filtered and washed with THF. The THF was evaporated and the residue was dissolved in DMSO. It was then purified on preparative LCMS using 0.1%NH4OH-CH3CN as a mobile phase. The pure fractions were collected and concentrated to obtain the desired compound as a purple solid (25mg, Yield 25%).

In a process analogous to Example 1 using appropriate starting materials, the corresponding compounds of Tables1-5 were prepared.

Example 2 (Compound 1, Table 6 and Compound 1. Table 71

4-(2-Dimethylamino-ethyl)-1 -methyl-3-phenyl-3,4-dihydro-1 H- benzo[g]quinoxaline- 2,5,10-trione (Compound 1 , Table 6) and 1-(2- Dimethylamino-ethyl)-4-methyl-3-phenyl-3,4-dihydro-1H-benzo[g]quinoxaline- 2,5,10-trione (Compound 1, Table 6)

To a solution of 1g of 2-chloro-N-(3-chloro-1,4-dioxo-1,4-dihydro-naphthalen- 2-yl)-N-methyl-2-phenyl-acetamide (2.7mmol, 1 equivalent) in 5 ml of anhydrous THF was added 1.2 ml of N, N-methylethylenediamine (10.7mmol, 4equivalents) in 1 ml of tetrahydrofuran. The mixture was stirred at room temperature for 10 minutes. To the mixture, approx. 100 mg of NaH (60%) was added until the color of the mixture turned to dark red. Reaction was monitored using TLC. After completion of the reaction, a quick purification of the reaction mixture was carried out by preparative LCMS using 0.1% Formic acid in acetonitrile as a mobile phase. The fractions with the desired mass were combined and evaporated. TLC showed that the residue contains two products. The residue was purified through a normal phase column using ethyl acetate and methanol as a mobile phase and both the products A and B were isolated as pure compounds. The titled compound A was collected as a red-purple solid (500mg, 48% yield). 1H NMR (CDCI3, 400MHz): δ 8.01 (dd, J=2.0Hz, 6.8Hz, 2H), 7.71 (m, 2H), 7.27 (m, 5H), 5.25 (s, 1H), 4.41 (m, 1H), 4.29 (m, 1H), 3.66 (m, 1H), 3.50 (s, 3H), 3.19 (m, 1H), 2.95 (brs, 3H), 2.87 (brs, 3H). 13C NMR (CDCI3, 400MHz): δ 181.9, 178.2, 163.2, 135.0, 134.4, 133.9, 133.4, 131.8, 130.9, 129.3, 128.8, 126.5, 126.3, 126.1 , 125.5, 66.9, 56.3, 49.1 , 44.3, 42.9, 33.7.

The titled compound B was collected as a purple solid (500mg, 48% yield). 1H NMR (CDCI3, 400MHz): .68.18 (d, J=7.2Hz, 1H), 7.98 (d, J=8.8Hz, 1H), 7.69 (m, 2H), 7.31 (m, 3H), 7.20 (m, 2H), 5.07 (s, 1H), 4.62 (m, 1H), 4.26

(m, 1H), 3.75 (m, 1H), 3.63 (s, 3H), 3.30 (m, 1H), 2.99 (brs, 3H), 2.92 (brs,

3H). 13C NMR (CDCI3, 400MHz): 6181.2, 177.3, 163.3, 136.6, 134.4, 134.2, 133.1, 131.8, 131.0, 129.4, 128.9, 126.3, 126.0, 125.5, 121.6, 68.9, 55.7, 44.1,43.1,42.2,41.0.

In a process analogous to Example 2 using appropriate starting materials, the corresponding compounds of Table 6 and Table 7 were prepared

Table 1

Table 2

Table 3

Table 4

Table 5

Table 6

Table 7

Table 8

Table 9

Table 10

Table 11

Table 12

Table 13

Table 14

Table 15

Claims

WHAT IS CLAIMED IS:
1. A compound having the structure of Formula (I)
Formula I wherein W, X, Y and Z are each independently selected from a CH, C-R4, C-R5, C-R6 C-R7, O (oxygen), N (nitrogen) or S (sulfur) and that no more than two W, X, Y and Z are O, N and S; wherein, R4, Rs, Re, and R each independently hydrogen, hydroxyl, sulfhydryl, alkoxy, thioalkoxy, alkyl, halogen, CN, CF3, NO2, COOR8, CONR8Rg, NR8R9, NR8COR9, NR8SO2R9, NRi0CONR8R9; wherein R8, Rg and Rio are independently hydrogen, alkyl, heteroalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyl, and heterocycloalkyl; NR8Rg is also substituted and unsubstituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; and wherein R8 and R-io can be connected together to form 4, 5,6 or 7-member cyclic ring system, R-i, R2 and R3 are independently H, alkyl, substituted and unsubstituted phenyl or polyaromatic, substituted and unsubstituted heteroaromatic, with hetero atom(s) as N, O, S, substituted and unsubstituted mono or polysubstituted aralkyl, substituted and unsubstituted cyclo or polycyclo hydrocarbon or mono or polyheterocycle of 3 to 8 ring atoms having one to four hetero atoms selected from N, O, or S ; and wherein substitutions are independently selected from hydrogen, hydroxyl, sulfhydryl, alkoxy, thioalkoxy, alkyl, halogen, CN, CF3, NO2, COOR8, CONR8R9, NR8R9, NR8COR9, NR8SO2R9, NRι0CONR8R9 wherein R8, R9 and R10 are independently as mentioned above; NR8R9 is also selected from substituted and unsubstituted mono or polycyclic ring with one to four heteroatoms such as N, O, S; and wherein R8 and R10 may be connected to form a 4, 5, 6 or 7-member cyclic ring system. i and R3 are also independently selected from:
NR13CONR14Ri5 :
-OR1
CONR13R14 wherein n is 2, 3, or 4 and Rn, R12, R13 and R14 are each independently selected from hydrogen, alkyl, cycloalkyl, substituted and unsubstituted aryl, substituted and unsubstituted heteroaryl, substituted and unsubstituted alkylaryl; NR13R14 is also substituted and unsubstituted mono or bicyclic ring with one to four heteroatoms such as N, O, S; and wherein Rn and R13 may be connected to form 4, 5,6 or 7- member cyclic ring system; R2 is also selected from:
- ;
R11 11 -G -NR13S02Ri4 -C — -OCONR14R15 -OR1 R12 R-I2
R11 R11 11 -C — -SR13 -C — -COOR13 -c — -CONR13R14 R12 R12 R12 wherein n is 0, 1, 2 and 3 and Rn, R12, R13 and R14 are independently selected from hydrogen, alkyl, substituted and unsubstituted cycloalkyl, substituted and unsubstituted aryl, substituted and unsubstituted alkaryl ; and wherein NR13R14 is also selected from substituted and unsubstituted mono or bicyclic ring with one to four heteroatoms selected from N, O, and S; and wherein Rn and R13 may be connected to form a 4, 5, 6 or 7 member ring system wherein n is 1, 2 or 3; including salts thereof. 2. The compound of claim 1 wherein W, X, Y and Z are each independently selected from CH, C-R4, C-R5, C-R6 C-R7, O, N or S and wherein no more than two of W, X, Y and Z are O, N and S and wherein, R4, R5, R6, and R7 each independently hydrogen, hydroxyl, sulfhydryl, lower alkoxy, (1-6 carbon atoms), lower thioalkoxy (1-6 carbon atoms), alkyl, halogen, CN, CF3, NO2, COOR8, CONR8Rg, NR8R9, NR8COR9, NR8SO2Rg, NR8CONR9Rιo and wherein R8, Rg and R10 are independently hydrogen, alkyl, H, alkyl, heteroalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyl, and heterocycloalkyl and wherein NR8Rg is also selected from substituted and unsubstituted mono or bicyclic ring, with one to four heteroatoms such as N, O, S; Ri, R and R3 are selected from H, alkyl of 1 to 6 carbon atoms, substituted and unsubstituted phenyl or polyaromatic, substituted and unsubstituted heteroaromatic, with hetero atoms selected from N, O, and S, substituted and unsubstituted aralkyl, substituted and unsubstituted cyclo or polycyclo hydrocarbon or mono or polyheterocycle of 3 to 8 ring atoms having one to four hetero atoms selected from N, O and S, and wherein substitutions are selected from hydrogen, hydroxyl, sulfhydryl, lower alkoxy, (1-6 carbon atoms), lower thioalkoxy (1-6 carbon atoms), alkyl, halogen, CN, CF3, NO2, COORs, CONR8R9, NR8R9, NR8CORg, NR8SO2R9, NRιoCONR8R9 wherein NR8Rg is also selected from a mono or polycyclic ring with one to four heteroatoms selected from N, O and S; and wherein R8 and R10 may be connected to form 4, 5,6 or 7-member cyclic ring system;
Ri and R3 are also independently selected from:
R11 R11 R11 -C— -NR13R14 i -c — -NR13COR14 -C — - 13CONRi4Ri5 : R-I2 R12 R12
wherein n is 2, 3, 4, 5 or 6 and Rn, Rι2, R13 and Ru are independently selected from hydrogen, alkyl, cycloalkyl, aryl, heteroaryl, alkylaryl from 7 to 10 carbon atoms; wherein NRι3Rι is also selected from mono or bicyclic ring with one to four heteroatoms selected from N, O and S, and wherein Rn and R-ι3 may be connected to form a 4, 5, 6 or 7-member cyclic ring system;
R2 is also selected from:
- ;
-OR13
NRι3R14 wherein n is 0, 1, 2, 3, 4 or 5 and Rn, R12, R13 and R14 are independently selected from hydrogen, alkyl, cycloalkyl, aryl, alkaryl from 7 to 10 carbon atoms, and NR13R-14 is also selected from a mono or bicyclic ring of one to four heteroatoms selected from N, O and S, and wherein Rn and Rι3 may be connected to form a 4, 5, 6 or 7 member ring wherein n is 1 , 2 or 3, including salts thereof.
3. The compound of claim 2 wherein W and Z are each independently CH, C-R , C-R7 or N and wherein X and Y are each independently C- R5 or C-R6.
4. The compound of claim 1 wherein X and Y are each independently C-R5, C-R6 or N and wherein W and Z are each independently C-R4 or C-R5.
5. The compound of claim 3 wherein W is C-R4 or N and wherein X, Y and Z are each independently C-R5, C-R6 or C-R7.
6. The compound of claim 3 wherein Z is C-R , C-R5, C-R7 or N and wherein W and Y are each independently C-R4, C-R6 or C-R7.
7. The compound of claim 4 wherein X is C-R5 or N and wherein W, Y and Z are each independently C-R4, C-Rβ or C-R .
8. The compound of claim 4 wherein Y is C-R4, C-R5, C-R6, C-R7 or N and wherein X and Z are each independently C-R , C-R5 or C-R7.
9. The compound of claim 8 wherein W X, Y and Z are each independently CH, C-R , C-R5, C-R6or C-R7.
10. The compound of claim 9 wherein each of W, X, Y and Z is CH. 11. The compound of claim 10 wherein Ri and R3 are selected from - hydrogen, -alkyl, cycloalkyl, unsubstituted or substituted phenyl, unsubstituted or substituted benzyl, -methylpyridine, -ethylpyridine, -mehtylindole, - ethylindole, alkoxyethyl-, hydroxyethyl, N,N-dialkyl-ehtyl, , N,N-dialkyl-propyl, methylpyrrole, ethylpyrrole, methylfuran, ethylfuran, -alkylmorpholine, - alkylpiperizine, -alkypiperidine, -alkylpyrrolidine, and R2 is H or lower alkyl.
12. Compounds of claim 1 wherein Ri is
wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
13. The compounds of claim 1 wherein R3 is wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
14. The compounds of claim 1 wherein Ri is
wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
15. The compounds of claim 1 wherein R3 is
wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
16. The compounds of claim 1 wherein R^ is
wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
17. The compounds of claim 1 wherein R3is wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
18. The compounds of claim 10 wherein Ri is
wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
19. The compounds of claim 10 wherein R3 is
wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
20. The compounds of claim 10 wherein Ri is
wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
21. The compounds of claim 10 wherein R3 is
wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
22. The compound of claim 10 wherein Ri is
R 11
-NR13S024
R12 wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
23. The compound of claim 10 wherein R3 is
wherein n is 2, 3 or 4 and R2 is H or lower alkyl.
24. A compound of claim 1 having a structure of Table 1 including salts thereof.
25. A compound of claim 1 having a structure of Table 2 including salts thereof.
26. A compound of claim 1 having a structure of Table 3 including salts thereof.
27. A compound of claim 1 having a structure of Table 4 including salts thereof.
28. A compound of claim 1 having a structure of Table 5 including salts thereof.
29. A compound of claim 1 having a structure of Table 6 including salts thereof. 30. A compound of claim 1 haying a structure of Table 7 including salts thereof.
31. A compound of claim 1 having a structure of Table 8 including salts thereof.
32. A compound of claim 1 having a structure of Table 9 including salts thereof.
33. A compound of claim 1 having a structure of Table 10 including salts thereof.
34. A compound of claim 1 having a structure of Table 11 including salts thereof. 35. A compound of claim 1 having a structure of Table 12 including salts thereof.
36. A compound of claim 1 having a structure of Table 13 including salts thereof.
37. A composition comprising a therapeutically effective amount of a compound of Claim 1 in a pharmaceutically acceptable carrier.
38. A method for preventing or treating a disease associated with a change in levels of expression of particular sets of genes in a mammal comprising administering to said mammal an effective amount of a compound of Claim 1.
39. A method for preventing or treating a disorder modulated by altered gene expression, wherein the disorder is selected from the group consisting of cancer, cardiovascular disorders, arthritis, osteoporosis, inflammation, periodontal disease and skin disorders, comprising administering to a mammal in need of such treatment or prevention a therapeutically effective amount of a compound of Claim 1.
40. The method of Claim 39, wherein the disorder is cancer, and the treatment prevents, arrests or reverts tumor growth, metastasis or both.
41. The method of Claim 39 wherein the cancer is colon cancer.
42. The method of claim 41 wherein said colon cancer is adenocarcinoma.
43. A gene set wherein expression of each member of said gene set is modulated as a result of treatment with a compound of claim 1. 44. The gene set of claim 43 wherein expression of each member of said gene set is increased or each member of said gene set is decreased as a result of said contacting.
45. The gene set of claim 43 wherein the members of said gene set are selected from the genes identified in Table 8. 46. The gene set of claim 43 wherein said gene set is present in a cell.
47. A set of genes comprising a plurality of subsets of genes wherein each subset of said plurality is a gene set identified by the method of claim 43. 48. A method for identifying an agent that modulates the expression of a gene set of claim 43, comprising: (a) contacting a compound with a test system containing one or more polynucleotides corresponding to each of the members of the gene set of claim 40 under conditions wherein the members of said gene set are being expressed; (b) determining a change in expression of each of said one or more polynucleotides of step (a) as a result of said contacting; wherein said change in expression in step (b) indicates modulation of the members of said gene set thereby identifying said test compound as an agent that modulates the expression of said gene set.
49. The method of claim 48 wherein said change in expression is a decrease in expression of said one or more polynucleotides. 50. The method of claim 48 wherein said change in expression is a change in transcription of said one or more polynucleotides.
51. The method of claim 48 wherein said change in expression is determined by determining a change in activity of a polypeptide encoded by said polynucleotide.
52. The method of claim 48 wherein said test system is a cell containing said polynucleotides.
53. The method of claim 51 wherein said cell is a cancer cell.
54. The method of claim 53 wherein said cancer cell is a colon cancer cell.
55. The method of claim 54 wherein said colon cancer cell is an adenocarcinoma cancer cell.
56. The method of claim 55 wherein said cell is a recombinant cell engineered to contain said set of genes. 57. Compounds identified as having activity using the method of claim
45.
58. The gene set of claim 43 wherein said gene set comprises a subset of the genes of Table 14.
59. The gene set of claim 43 wherein said gene set comprises a subset of the genes of Table 15.
60. The method of claim 48 wherein said compound modulates the expression of a subset of genes of Table 15.
I ll
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US8344104B2 (en) 2006-05-11 2013-01-01 Quark Pharmaceuticals, Inc. Screening systems utilizing RTP801
US7723052B2 (en) 2006-05-11 2010-05-25 Quark Pharmaceuticals, Inc. Screening systems utilizing RTP801
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