Coumermycin analogs as chemical dimerizers of chimeric proteins

FIELD OF THE INVENTION

[0001] The present invention is directed to coumermycin derivatives useful for promoting the dimerization of chimeric signaling, intracellular proteins.

BACKGROUND OF THE INVENTION

[0002] Signal transduction is the process by which extracellular molecules influence intracellular events. A cellular response generally involves multiple signal transduction cascades that operate in concert to elicit a specific biological response. Activities of signal transduction pathways can be regulated through the use of biological molecules, i.e. protein kinases. While many of the proteins in these pathways are known, little is understood about the relationship between particular signal transduction pathways.

[0003] In U.S. Pat. No. 5,830,462, issued Nov. 3, 1998; and U.S. Pat. No. 5,834,266, issued Nov. 10, 1998, both to Crabtree et al (both incorporated herein by reference hereto), a general procedure for the regulation of dimerization and oligomerization of intracellular proteins as biological, control mechanisms is suggested. Crabtree further teaches that many signaling pathways originate with the binding of extracellular ligands to cell surface receptors, and receptor dimerization can lead to transphosphorylation and the recruitment of proteins that continue the signal transduction cascade.

[0004] In “Activation of the Raf-1 Kinase Cascade by Coumermycin Induced Dimerization,” Farrar, M. A., Alberola-Ila, J. and Perlmutter, R. M., Nature, Vol. 383, pp. 178-181, Sep. 12, 1996 (incorporated herein by reference hereto), the carboxy terminus of Raf-1 serine/threonine kinase was covalently attached to the amino terminus of the B subunit of bacterial DNA gyrase (GyrB). Streptomyces derived natural products, coumermycin and novobiocin, are known to bind GyrB with strong affinity. The region that binds the protein is known to be an oligosaccharide (also known as noviose sugar) and the attached coumarin, a common element between the 2 structures. The stoichiometry of binding between GyrB and drug is 2:1 for coumermycin and 1:1 for novobiocin.

[0005] Farrar et al suggests adding coumermycin to the chimeric Raf-GyrB fusion protein wherein, coumermycin bound 2 molecules of GyrB that concomitantly brought the 2 Raf kinases into close proximity to one another. This close proximity induced Raf dimerization and led to activation of the Raf kinase cascade.

[0006] Furthermore, Farrar et al teaches that if a sufficient concentration of novobiocin is added to the coumermycin/GyrB/Raf complex, coumermycin can be displaced from the GyrB active site having similar binding constants and block kinase activation.

[0007] Coumermycin is known to have induced dimerization of the tyrosine kinase, Jak2, as well as the transcription factors STAT3, STAT5a, and STAT5b. Unfortunately, it has failed to activate a number of other proteins involved in signal transduction. It is believed that GyrB-Coumermycin-GyrB complex can not orient all kinases and transcript factors into the proper orientation for cross-phosphorylation. A coumermycin analog with a more flexible or longer spacing group will result in the activation of additional signaling proteins, and might have enhanced cellular penetration and potency than coumermycin.

SUMMARY OF THE INVENTION

[0008] The present invention is directed to coumermycin analogs of general formula I:

[0009] or a pharmaceutically acceptable salt or ester thereof,

[0010] wherein X is a linking group that connects the two halves of the molecule.

DETAILED DESCRIPTION OF THE INVENTION

[0011] The present invention is described herein in detail using the terms defined below unless otherwise specified.

[0012] As used herein the term “alkyl” refers to a monovalent alkane (hydrocarbon) derived radical containing from 1 to 18 carbon atoms. It can be straight, branched, or cyclic. Preferred alkyl groups include methyl, ethyl, propyl, isopropyl, butyl, t-butyl, cyclopentyl and cyclohexyl. When the alkyl group is said to be substituted with an alkyl group, this is used interchangeably with “branched alkyl group”.

[0013] The term “aryl” refers to aromatic rings, e.g., phenyl, substituted phenyl and the like, as well as rings which are fused, e.g., naphthyl, phenanthrenyl and the like. An aryl group thus contains at least one ring having at least 6 atoms, with up to five such rings being present, containing up to 22 atoms therein, with alternating (resonating) double bonds between adjacent carbon atoms or suitable heteroatoms. The preferred aryl groups are phenyl, naphthyl and phenanthrenyl. Aryl groups may likewise be substituted as defined. Preferred substituted aryls include phenyl and naphthyl.

[0014] The term “diaryl” refers to two aromatic rings linked together.

[0015] The phrase “alkyl with heteroatoms in the chain” refers to alkyl substituents having one or more altered or continuing oxygen, sulfur or nitrogen atom in the chain replacing carbon atoms.

[0016] The term “cyclic alkyl” or “cycloalkyl” refers to a specie of alkyl containing from 3 to 18 carbon atoms, without alternating or resonating double bonds between carbon atoms. It may contain from 1 to 4 rings which are fused. Preferred cyclic alkyls are organic substituents having only one ring structure containing alkyl groups therein or having two fused, cyclic ring structures containing alkyl groups therein.

[0017] The phrase “combination of alkyl, aryl and heteroaryl” refers to substituents that contain various at least two of the referenced substituents in combination.

[0018] The term “heteroatoms” refers to O S or N, selected on an independent basis.

[0019] The term “heteroaryl” refers to a monocyclic aromatic hydrocarbon group having 5 or 6 ring atoms, or a bicyclic aromatic group having 8 to 10 atoms, containing at least one heteroatom, O, S or N, in which a carbon or nitrogen atom is the point of attachment, and in which one or two additional carbon atoms are optionally replaced by a heteroatom selected from O or S, and in which from 1 to 3 additional carbon atoms are optionally replaced by nitrogen heteroatoms, said heteroaryl group being optionally substituted as described herein. Examples of this type are pyrrole, pyridine, oxazole, thiazole and oxazine. Additional nitrogen atoms may be present together with the first nitrogen and oxygen or sulfur, giving, e.g., thiadiazole. Examples include the following:

[0020] The present invention is directed to coumermycin analogs, pharmaceutically-acceptable esters and salts thereof of general formula I:

[0021] wherein X, a linking group that connects the two halves of the molecule may contain from about 1 to about 54 atoms. The linking group, X, may be selected from alkyl, aryl, diaryl, substituted alkyl, substituted aryl, diaryl, substituted alkyl, alkyl with hereroatoms in the chain, heteroaryl, cyclic and bicyclic alkyl, and a combination of alkyl, aryl and heteroaryl substituents. Optionally, the linking group may also be selected from pyrrole, pyridine, furan, indole, benzofuran, dibenzofuran, thiophene, straight chain alkyl, cycloalkyl, phenyl, diaryl, derivatives and combinations thereof. The pyrrole moiety may be selected from the following:

[0022] wherein R3 is H or CH3.

[0023] The diaryl moiety may be selected from the following:

[0024] The pyridine moiety may be selected from the following:

[0025] The straight alkyl chain may contain from about 1 to about 18 carbon atoms therein.

[0026] The indole moiety may be selected from the following:

[0027] The benzofuran moiety may be selected from the following:

[0028] The phenyl moiety may be selected from the following:

[0029] The cycloalkyl moiety may be selected from the following:

[0030] The furanyl moiety may be selected from the following:

[0031] The dibenzofuranyl moiety may be selected from the following:

[0032] The analogs are suitable for use as chemical dimerizers oligomerizers of chimeric proteins.

[0033] The coumermycin analogs of the present invention are useful as chemical dimerizers of chimeric protein kinases or transcription factors. The analogs are capable of covalently attaching the carboxy terminus of Raf-1 serine/threonine kinase to the amino terminus of the B subunit of bacterial DNA gyrase (GyrB).

[0034] Coumermycin is a natural product known to be useful in the inhibition of amino-terminal 24K subdomain of the B subunit of bacterial DNA gyrase (GyrB).

[0035] Analogs of coumermycin may be prepared in accordance with the chemical synthesis sequence from commercially available materials, as presented herein.

[0036] In the present invention, organic molecules regulate signal transduction pathways by activities, among others, proteins or transcription factors. A natural molecule, coumermycin, simultaneously binds two (2) molecules of a B subunit of bacterial DNA gyrase (GyrB) which are, in turn, covalently linked to Raf-1 kinase. The binding event brings the 2 chimeric proteins in close proximity to one another and promotes dimerization (or phosphorylation) of the 2 Raf-1 enzymes which activates a signal transduction pathway. A monomeric natural product, novobiocin, binds just one of these GyrB-Raf-1 chimers and prevents (or turns off) the signaling cascade. Unfortunately the coumermycin/GyrB system can activate only a select few kinase systems. It is, therefore necessary to prepare coumermycin analogs that will induce cross-phosphorylation in a more general manner.

[0037] The present invention is further directed to a method of chemically dimerizing chimeric proteins utilizing a coumermycin analog of general formula I:

[0038] wherein X is a linking group selected from straight, branched and cyclic alkyl, aryl, diaryl, substituted aryl, diaryl, substituted alkyl, alkyl with heteroatoms in the chain, heteroaryl, a combination of alkyl, aryl, heteroaryl, pyridine, furan, indole, benzofuran, dibenzofuran, thiophene, straight chain alkyl, cycloalkyl, phenyl, diaryl and combinations thereof.

[0039] Examples of coumermycin analogs may be selected from the following

1CompoundNo.Structure1

Synthesis Schemes

[0040] The compounds of this invention can be synthesized by methods known in the art. As illustrated herein, the compounds can be synthesized in accordance with Synthesis Schemes I through V.

[0041] Those skilled in the art will appreciate other methods thereof after reviewing the following:

[0042] A protected version of the noviose sugar (1) is prepared by exposing commercially available novobiocin to a Lewis acid or protic acid, preferably a strong protic acid, more preferably toluenesulfonic acid in the presence of acetone. Hydrolysis of the C-3′ carbamate moiety is accomplished by stirring with hydroxide, preferably lithium hydroxide, to give 2. The C-3′ position of the sugar was acylated by exposing 2 to a derivative of 5-methyl pyrrole-2-carboxylic acid where the carboxylic acid is activated for acylation. Preferably the pyrrole is activated as an anhydride (see compound 7 in Scheme II) and preferably an acylation catalyst is used, more preferably the acylation catalyst is tributyl phosphine. Protected sugar 3 is converted to the reducing sugar 4 by exposure to acid, preferably trifluoroacetic acid.

[0043] A stirring mixture of novobiocin (12.0 g), p-toluenesulfonic acid (3.6 g) in 100 mL anhydrous acetone was heated to 48° C. A white precipitate formed during course of the reaction. After six hours, the cloudy white solution was cooled to room temperature and the acetone was removed in vacuo. The resulting solid was purified by column chromatography (basic alumina, 100% ethyl acetate) to give 3.2 g of the protected noviose sugar 1. Mass spectra (MS) (ESI) m/z=298 (M+Na+).

[0044] Sugar acetonide 1 (2.5 g) was dissolved in 30 mL methanol and 30 mL THF (tetrahydrofuran). Lithium hydroxide hydrate (2.9 g) was dissolved in 30 ml of water and added to the stirring solution. The solution was warmed to 40° C. and stirred overnight. The product 2 was extracted with water and ethyl acetate (3×). No purification was necessary. MS (ESI) m/z=255 (M+Na+).

[0045] Noviose sugar (0.82 g) 2 and pyrrole anhydride 7 (1.6 g) were dissolved in 50 mL of dry methylene chloride and stirred at room temperature under nitrogen.

[0046] Tributylphosphine (0.77 g) was added and the solution was stirred for 60 hours. The solution was added to 30 mL water and extracted twice with methylene chloride. The organic layers were combined, dried over magnesium sulfate, filtered, and dried in vacuo. The crude sugar was purified by silica gel chromatography (20%→25%→33% ethyl acetate in hexane) to provide the acylated noviose 3 (0.99 g). MS (ESI) m/z=362 (M+Na+).

[0047] The protected noviose (513 mg) was dissolved in a 4:1 mixture of trifluoroacetic acid (TFA):water (5 mL) and stirred at room temperature for five minutes. The solvents were removed in vacuo and the resulting solid was filtered through silica gel (100% ethyl acetate). The purified reducing sugar 4 was obtained as a mixture of anomers (381 mg). MS (ESI) m/z=322 (M+Na+).

[0048] Syntheses of 5-methylpyrrole-2-carboxylic acid and its derivatives are well known in the literature. We found the method of Curran, T. P., Keaney, M. T. J. Org. Chem. 61, 9068 (1996) to be preferred. Mixing ethyl acetamidomalonate and 1,4-dichloro-2-butyne in the presence of base, preferably sodium ethoxide, provided pyrrole ester 5. Hydrolysis in the presence of hydroxide, preferably lithium hydroxide gave the desired carboxylic acid 6. Activation of the carboxylic acid 6 was accomplished by exposing the carboxylic acid to a peptide coupling reagent, preferably a carbodiimide, more preferably 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride. The anhydride product 7 can be used in Scheme I to acylate the noviose sugar fragment 2.

[0049] The procedure of Curran, T. P., Keaney, M. T. J. Org. Chem. 61, 9068 (1996) was followed. Diethyl acetamidomalonate (0.395 g) was added to a solution of sodium ethoxide in ethanol (1.0 M, 9 mL) and the solution was heated to reflux (95° C. to 97° C.). 1,4-dichloro-2-butyne (190 μL) was added and the solution was refluxed for one hour. Additional portions of 1,4-dichloro-2-butyne (190 μL) and sodium ethoxide in ethanol (0.70 mL, 21 wt. %) were added and heating continued for another hour. When complete, the solution was cooled to room temperature and the ethanol was removed in vacuo. The brown residue was dissolved in ethyl acetate and extracted water (2×), saturated sodium bicarbonate (3×), IN HCl (3×), and brine. The organic layer was dried over magnesium sulfate, filtered and evaporated. The resulting solid was purified by column chromatography (silica gel, 10% ethyl acetate in hexane) to give 130 mg of the ethyl ester 5. MS (ESI) m/z=154 (M+H+).

[0050] The ethyl ester 5 (4.5 g) was dissolved in methanol (50 mL) and THF (50 mL). Lithium hydroxide hydrate (10.0 g) was dissolved in water (50 mL) and added to the stirring solution. The reaction was stirred overnight at 40° C. The crude product was added to dilute aqueous HCl (pH between 1.5-3.0) and extracted with ethyl acetate (3×). The organic layers were combined, dried over magnesium sulfate, and filtered and evaporated to give 6 (3.6 g). No purification was necessary.

[0051] 5-methyl-pyrrole-2-carboxylic acid 6 (4.8 g) was dissolved in methylene chloride (150 mL) and stirred at room temperature under nitrogen. 4-methylmorpholine (2.11 mL) was added followed by 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (3.68 g). After stirring for two hours, the crude material was added to water and extracted with methylene chloride (3×). The organic layers were combined, dried over magnesium sulfate, filtered, and dried in vacuo. The product was purified by column chromatography (silica gel, 33% ethyl acetate/ 67% hexane) and provided the desired anhydride 7 (3.65 g). MS (ESI) m/z=233 (M+H+).

SCHEME III

Synthesis of the Coumarin Fragment

[0052] A number of literature procedures exist for the synthesis of the coumarin core of coumermycin. The method of Laurin, P. et al., Bioorg. Med. Chem Lett. 9, 2079 (1999) and Haesslein, J -L. et al. WO 99/35155 is preferred. Commercially available 2,4-dihydroxy-3-methylacetophenone was selectively protected with dihydropyran is the presence of acid, preferably toluenesulfonic acid, to provide 8. The coumarin fragment 9 was prepared by exposure to an appropriate electrophile, preferably diethyl carbonate, to in the presence of base. Protection of 9 was accomplished addition of diphenyl diazomethane to form 10. Removal of the tetrahydropyranyl protecting group occurred in the presence of water under acid catalysis to yield compound 11.

[0053] The procedure of Laurin, P. et al., Bioorg. Med. Chem Lett. 9, 2079 (1999) was followed. Anhydrous diethyl ether (130 mL) was added to 2,4-dihydroxy-3-methylacetophenone (21.52 g). The mixture was stirred under nitrogen and dihydropyran (21.5 mL) was added. The mixture was cooled to 0° C. Toluenesulfonic acid (118 mg) was added and the reaction was allowed to slowly warm to room temperature. After twelve hours another portion of toluenesulfonic acid (80 mg) was added. The black solution was stirred an additional six hours and then added to a saturated sodium bicarbonate solution. Extraction with ether followed by drying over magnesium sulfate, filtration and solvent removal provided a black solid which was purified by column chromatography (Silica gel, 20%→25%→33% ethyl acetate in hexane) to provide the protected acetophenone 8 (15.9 g). MS (ESI) m/z=251 (M+H+)

[0054] The procedure of Laurin, P. et al., Bioorg. Med. Chem Lett. 9, 2079 (1999) was followed. Protected acetophenone 8 (15.9 g) was dissolved in toluene (170 mL). Diethyl carbonate was added and the solution was heated to 90° C. under nitrogen with vigorous stirring. Sodium hydride (60% in mineral oil, 5.87 g) was added portionwise to prevent foaming. Stirred at 90° C. overnight. Cooled to room temperature and an off-white solid was collected after centrifugation. The solid was triturated with ether, 1M NaH2PO4, water, acetone, and ether again and the resulting sodium salt of the coumarin was collected as a white solid. The coumarin was dissolved in methanol and acidified with acetic acid. Water was added and the methanol was removed in vacuo. The white precipitate was collected by filtration and dried to give the desired coumarin 9. MS (ESI) m/z=277 (M+H+)

[0055] The procedure of Laurin, P. et al., Bioorg. Med. Chem Lett. 9, 2079 (1999) was followed. The coumarin 9 (2.85 g) was dissolved in dimethyl formamide (DMF) (13 mL) and warmed to 90° C. under nitrogen. Diphenyl diazomethane (3 g) was dissolved in DMF (13 mL) and added dropwise to the reaction mixture over 150 minutes. After two hours additional diphenyl diazomethane (400 mg) was added. After two more hours diphenyl diazomethane (400 mg) was added again. Stirred an additional 6 hours at 90° C. The solution was cooled to room temperature and added to water. After extraction with ethyl acetate (3×) the organic layers were combined, dried over magnesium sulfate, filtered and evaporated in vacuo. The crude mixture was chromatographed (silica gel, 100% methylene chloride→1%→2%→3%→4%→5%→50%→100% ethyl acetate in ethyl acetate in methylene chloride) to provide the fully protected coumarin 10 (2.77 g). MS (ESI) m/z=443 (M+H+)

[0056] The procedure of Laurin, P. et al., Bioorg. Med. Chem Lett. 9, 2079 (1999) was followed. The coumarin 10 (2.77 g) was dissolved in anhydrous methylene chloride (20 mL) and anhydrous methanol (20 mL) and stirred at room temperature under nitrogen. Acetyl chloride (0.31 mL) was slowly dissolved in anhydrous methanol (5 mL) and added to the stirring solution of coumarin. After 90 minutes a white precipitate formed. The mixture was neutralized with aqueous saturated sodium bicarbonate and extracted with methylene chloride. The organic layer was dried over magnesium sulfate, filtered and evaporated. The coumarin 11 was purified by trituration with ethyl acetate. MS (ESI) m/z=359 (M+H+).

[0057] The pyrrole-sugar fragment 4 and the coumarin fragment 11 were coupled to form fragment 12. Preferably they were coupled using an azodicarboxylate and a phosphine derivative, more preferably they were coupled using diisopropylazodicarboxylate and triphenyl phosphine. The protecting group of 12 was removed by hydrogenolysis, preferably hydrogen gas in the presence of palladium, to provide 13. Diazotizaton of 13 with diazobenzene provided 14 that was reduced to the PNC-amine, (PNC=3-amino-4-hydroxy-8-methyl-7-[[3-O-[(5-methyl-2-pyrrolyl)carbonyl]noviosyl]oxy]coumarin) preferably with sodium dithionite.

[0058] The PNC-amine is a late-stage building block that can be readily converted to the natural product coumermycin and many other dimeric coumarin derivatives, including those in the illustrated examples and in the claims section hereof.

[0059] The procedure of Laurin, P. et al., Bioorg. Med. Chem Lett. 9, 2079 (1999) was followed. The coumarin 11 (123 mg) and reducing sugar 4 (82.6 mg) were suspended in methylene chloride (5 mL) and stirred at room temperature under nitrogen. Triphenyl phosphine (101 mg) was added followed dropwise addition of diisopropyl azodicarboxylate (0.087 mL in 0.40 mL methylene chloride). After two hours, additional portions of triphenyl phosphine (36 mg) and diisopropyl azodicarboxylate (0.027) were added. Stirred under nitrogen overnight. Worked up by evaporation of methylene chloride in vacuo. Purified by repeated chormatography in silica gel (25%→33%→50% ethyl acetate in hexanes) to give the desired α-glycoside 12 (73 mg) and the undesired β-glycoside (32.6 mg). MS (ESI) m/z=640 (M+H+).

[0060] The α-glycoside 12 (73 mg) was dissolved in THF (2.5 mL) and ethanol (2.5 mL). Palladium on Carbon (10%, 14 mg) was added and the solution degassed. One atmosphere of hydrogen gas added and the reaction was stirred overnight. Hydrogen gas was removed in vacuo and the solution was filtered though celite. The eluant was evaporated and the solid 13 was taken crude to the next step. MS (ESI) m/z=474 (M+H+).

[0061] Aniline (0.10 mL) was added to a stirring solution of aqueous HCl (IN, 3.84 mL) at 0° C. Sodium nitrite was dissolved in water (0.35 mL) and added dropwise to the aniline solution. After 10 minutes, an aqueous solution of sodium acetate (405 mg in 0.70 mL water) was added and the resulting diazo benzene was stirred 10 additional minutes at 0° C. The noviose-coumarin 13 was dissolved in methanol (3 mL) and THF (1 mL) and stirred at room temperature. One equivalent of the diazobenzene solution was added dropwise to the coumarin and the solution turned a deep orange. The product was added to a saturated aqueous ammonium chloride solution and extracted with ethyl acetate (3×). The organic layers were combined, dried over 15 magnesium sulfate and evaporated. The product 14 was taken to the next step without further purification. MS (ESI) m/z=578 (M+H+).

[0062] The diazotized coumarin 14 was dissolved in THF (3 mL) and Ethanol (6 mL). The solution was stirred at room temperature and sodium acetate (56 mg dissolved in 1 mL water) was added. Sodium dithionate (80 mg) was then added and the solution turned from dark orange to light yellow. The solvents were then dried in vacuo and resulting crude PNC-amine was purified by silica gel chromoatography. (1:9:90 ammonium hydroxide: methanol: methylene chloride→2:18:80→3:27:70) to give pure PNC-amine (48.1 mg). MS (ESI) m/z=489 (M+H+).

[0063] The coumarin analogs were prepared by the method shown in Scheme V. The PNC-Amine was exposed to a dicarboxylic acid or a derivative thereof to yield coumarin derivatives such as 15 and 16. Preferably, the PNC-Amine was exposed to a dicarboxylic acid and a peptide coupling reagent, most preferably the peptide coupling reagent was O-(azabenzotriazole-1-yl) N,N,N′,N′-tetramethyluronium hexafluorophosphate).

[0064] Chelidonic acid (2.9 mg) and O-(azabenzotriazole-1-yl) N,N,N′,N′-tetramethyluronium hexafluorophosphate) (14.2 mg) were dissolved in dry deoxygenated DMF (1 mL) and stirred at room temperature under argon. 4-methylmorpholine (10.0 mL) was added to the reaction. After 15 minutes, PNC-amine (21.4 mg) was dissolved in dry deoxygenated DMF (0.4 mL) and added slowly to the activated diacid. The reaction was stirred overnight over argon and after 12 hours, the crude DMF solution was purified by injecting the solution onto the HPLC column where the final product 15 (3.3 mg) was readily purified (RP18, gradient, 90% H2O→100% acetonitrile). MS (ESI) m/z=1125 (M+H+).

[0065] 4,4;-oxybis(benzoic acid) (4.5 mg) and O-(azabenzotriazole-1-yl) N,N,N′,N′-tetramethyluronium hexafluorophosphate) (13.2 mg) were dissolved in dry deoxygenated DMF (1 mL) and stirred at room temperature under argon. 4-methylmorpholine (10.5 μL) was added to the reaction. After 15 minutes, PNC-amine (23.6 mg) was dissolved in dry deoxygenated DMF (0.3 mL) and added slowly to the activated diacid. The reaction was stirred overnight over argon and after 12 hours, the crude DMF solution was purified by injecting the solution on to an HPLC column where the final product 16 was readily purified (RP18, gradient, 90% H2O→100% acetonitrile). MS (ESI) m/z=1199 (M+H+). Other coumermycin analogs were prepared using an identical method.

BIOLOGICAL EVALUATION

[0066] To evaluate the effectiveness of the analogs of the present invention to act as chemical dimerizers of chimeric proteins, a BAF cell proliferation assay was performed.

BAF Cell Proliferation Assay

[0067] BAF cells are known in the art and are a murine cell line that is dependent on cytokine stimulation for growth. We have transfected BAF Cells with the human IL2 Receptor β chain. These transfected cells respond to human IL-2 by increasing their rate of cellular proliferation. This can be assayed by measuring the amount of tritiated thymidine that these cells incorporate into their DNA. One of the signaling proteins activated by IL-2 is the transcription factor STAT5b. This activation of STAT5b is responsible, in part, for the growth-promoting effects of IL-2.

[0068] STAT5b is activated by dimerization, an event that is dependent on its phosphorylation and which requires interaction of STAT5b with a ligand bound activated receptor. We can mimic this activation of STAT5b by transfecting BAF cells with a fusion protein consisting of the GyrB domain (the24 kDa amino-terminal fragment of bacterial DNA gyrase, amino acids 2-220) fused to the carboxy-terminus of STAT5b. Addition of the symmetrically dimeric antibiotic coumermycin artificially forces the dimerization of STAT5b-GyrB fusion proteins and results in an increased rate of cell growth that can be measured by the cell's ability to incorporate thymidine. This provides an assay to determine the ability of coumermycin analogs to promote dimerization of STAT5b-GyrB fusion proteins.

[0069] The assay is run as follows: BAF cells transfected with the human IL-2 receptor β chain and STAT5b-GyrB are washed twice in phosphate-buffered saline. They are then re-suspended in BAF cell media that lacks IL-2 and placed in a 96-well plate. Increasing amounts of coumermycin, or coumermycin analogs are then added to different wells in a 96-well plate and the cells are incubated overnight. Twenty-four hours later the cell media is spiked with tritiated thymidine and the cells are incubated for an additional 16 hours. The cells are subsequently harvested with a Wallac cell harvester and the amount of tritiated thymidine incorporated is measured using a β scintillation counter.

EXAMPLES

[0070] The following examples are for the purpose of illustration of the invention, and in no way are meant to limit or deter the scope of the invention. Those skilled in the art, after reviewing the examples, will appreciate other, various methods in which the invention can be practiced.

[0071] The abbreviations used in the examples are as follows:

[0072] STAT=Signal Transducer and Activator of Transcription

[0073] IL=Interleukin as in Interleukin-2 (IL2)

[0074] PBS=Phosphate buffered saline

[0075] DMSO=Dimethyl Sulfoxide

[0076] BAF media

[0077] NEAA=Non-Essential Amino Acids

[0078] RPMI=cell growth media (Roswell Park Memorial Institute medium)

[0079] FCS=fetal calf serum

[0080] L-glu=the L form for glutamine

[0081] P/S=penicillin and streptomycin

Example 1

[0082] Compounds 5 and 6 were tested for BAF cell proliferation. Set up for BAF proliferation assay was as follows:

[0083] Spin down cells and wash one time in PBS. Resuspended in BAF cell media without cytokine at 2×105 cells/ml. added 100 μl/well or 2×104 cells. The compounds were prepared at 2 mg/ml (equivalent to 1.8 nM±5%). Plates were set up so that each condition equaled 1 row of 12 (n=number of wells/row=12). DMSO being utilized as an initial control Compound 5 was prepared in concentrations of 1.6, 16, 163, 450, and 900 nM, and 1.8 μM in DMSO, and as a second control, IL-2 growth factor was added to coumermycin. Two novenamine anologs, Comparative Compounds (CCmpd) 1 and 2, below were also use in this example as control. It is known that novenamine analogs penetrate BAF cells poorly. The comparative novenamine compounds are as follows:

[0084] Table 2 provides the concentration for the coumermycin control and compounds, as well as the proliferation results and number of wells/row (n) of the microplate.

2TABLE 2Proliferation of STAT5b-GyrB Transfected BAF Cells Following Stimulation withCoumermycin or Coumermycin Analogs12345678910StimulusConc.Prolif.S.D.nStimulusConc.Prolif.S.D. 2NDMSO0.115977254912DMSO0.116215118112Cou. 161.616137109012Cmpd 5 1.61.615270115712nMnMCou. 16.31.616261134212Cmpd 5 16.31614277136612nMnMCou. 16316316836301712Cmpd 5 16316314139118212nMnMCou. 45045018842204612Cmpd 5 45045012732101012nMnMCou.90021057123911Cmpd 5 9009001231594112900 nMnMCou. 1.8180023199140211Cmpd 5 1.818001175196012μMμMIL-2103613723112IL-21044071098912DMSO0.115971133510DMSO0.11729695012Cmpd 61.61495482812CCmpd 21.614761819111.6 nM1.6 nMCmpd 6161471096312CCmpd 2161445921011216.3 nM16.3 nMCmpd 61631335188412CCmpd 216314516123912163 nM163 nMCmpd 64501219092911CCmpd 245013568142812450 nM450 nMCmpd 69001287289012CCmpd 29001228163012900 nM900 nMCmpd 618001083257212CCmpd 21800116761025121.8 μM1.8 μMIL-2108500706912IL-2109880503312DMSO0.116755126912CCmpd 11.6157411283121.6 nMCCmpd 1161469113541216.3 nMCCmpd 116313628179612163 nMCCmpd 145012465110812450 nMCCmpd 19001193590112900 nMCCmpd 1180011057901121.8 μMIL-2104616480712

Example 2

[0085] In this example, Compounds 3, 4, 7, 8 and 9 were tested in BAF cell assays. The compounds were re-suspended in dimethylsulfoxide (DMSO) at a concentration of 2 mg/ml. Compounds 7 and 9 appeared slightly “purple” after dissolving in DMSO, perhaps a suggestion of some contamination with PNC-Amine. Next, the cells were washed 2 times with PBS. The re-suspended cells were present at a concentration of 1×105 cells /ml in BAF media (RPMI, 10% FCS (fetal calf serum), 1% NEAA (non-essential amino acid), 1% L-G-lu, P/S and Hepes) without IL-2, added 100 μl to well (equal to 1×104 cells/well).

[0086] The compounds were prepared in as follows: DMSO was used as a control; each of the 5 compounds were combined with DMSO at concentrations of 1.8 μM, 900 nM, 450 nM, 90 nM 9 nM, and 900 nM. As a second control, coumermycin in IL-2 was utilized. Each solution at the aforementioned concentration condition, along with BAF cells, was placed in 1 row (12 wells) of a 96 well plate. Thereafter, 100 μL of compound (twice the concentration) was added to the wells. After 24 hours, 3-H thymidine was added to the wells, and the assays were harvested.

[0087] Table 3 provides the DMSO concentration for the coumermycin control and compounds, as well as the proliferation results and number of wells/row (n) of the microplate.

3TABLE 3Proliferation of STAT5b-GyrB Transfected BAF Cells Following Stimulationwith Coumermycin or Coumermycin Analogs2371Conc.Prolif.456Prolif.89Compound(graph)(cpmS.D.NCompound(cpm)S.D. 2NDMSO0.0920912151472DMSO20912151472Cou. 900 pM0.918071169012Cmpd 8 90179731657pMCou. 9 nM920551190312Cmpd 8 9193771209nMCou. 90 nM9025219115912Cmpd 8207151860900 nMCou. 450 nM45027515190712Cmpd 8229361241450 nMCou. 900 nM90030752174312Cmpd 8238581276900 nMCou. 1.8 μM180030664195012Cmpd 82277218061.8 μMIL-298745707372IL-298745707372DMSO0.0920912151472DMSO20912151472Cmpd 90.9168261703Cmpd 7 900165201628900 nMpMCmpd 9 9918126984Cmpd 7165991617nM9 nMCmpd 9 9090191771495Cmpd 7 90176901562nMnMCmpd 9450208891588Cmpd 7205531402450 nM450 nMCmpd 9 900900222102013Cmpd 7206191563μM900 nMCmpd 9 1.81800203671428Cmpd 7202071598μM1.8 μMIL-298745707372IL-298745707372DMSO0.0920912151472DMSO20912151472Cmpd 3 9000.9163131836Cmpd 4 900202041825Cmpd 3 99167671622Cmpd 4 9192902532nMnMCmpd 3 9090199201482Cmpd 4 90197311856nMnMCmpd 3 90450222211967Cmpd 4 450207261756nMnMCmpd 3 900900228242140Cmpd 4 900228172099nMnML880,0781800213891761Cmpd 4 1.8231351411.8 μMμMIL-298745707372IL-298745707372

Example 3

[0088] A proliferation assay of Compound 1 using BAF cells transfected with the human growth factor IL-2RB chain and STAT5b-GyrB.

[0089] The assay was set up using DMSO; Compound 1 in DMSO concentrations of 900 pM, 9 nM, 90 nM, 450 nM, 900 nM, and 1.8 μM; and IL-2, as a control. Compound 1, in rows of 12, containing the aforementioned concentrations of DMSO, coumermycin controls, and the cells were placed in wells of a microplate. After 24 hours 3H-thymidine at various concentrations was added to each well and allowed to proliferate.

[0090] Table 4 provides the DMSO concentration for the coumermycin control and compounds, as well as the proliferation results and number of wells/row (n) of the microplate.

4TABLE 4Proliferation of STAT5b-GyrB Transfected BAF Cells FollowingStimulation with Coumermycin or Coumermycin AnalogsConc.Cou.Cmpd 1Conc.(graph)Prolif.S.D.nProlifS.D. 2NDMSO0808548524808548524900 pM0.97422299127156773129 nM987924691276534091290 nM90986031912748744012450 nM4501083242212720929212900 nM90011470750127092344111.8 μM18001230861812639731312IL-23164420052431644200524

Example 4

[0091] A proliferation assay of Compound 2 using BAF cells transfected with the human growth factor IL-2Rβ chain and STAT5b-GyrB.

[0092] The cells were placed in the wells at a concentration of 1×104 cells/well (in 100 μL=1×105 cells/mL. The assay was set up using DMSO; Compound 2 in DMSO concentrations of 900 pM, 9 nM, 90 nM, 450 nM, 900 nM, and 1.8 μM; and IL-2, as a control. Compound 2, in rows of 12, containing the aforementioned concentrations of DMSO, coumermycin controls, and the BAF cells were placed in wells of a microplate. After 24 hours 3H-thymidine was added to each well and the cells were allowed to proliferate an additional 16 hours. FIG. 12 provides a graphical illustration of the results of the proliferation.

[0093] An inhibition assay was also conducted for Compounds 1 and 2. For this assay, all wells contained a DMSO concentration of 90 nM of coumermycin. Compounds 1 and 2 were added at concentrations of 1.8 μM, 900 nM, 90 nM and 9 nM. The conditions of the assay were identical to those referenced early in this example, except that one-third of the amount of 3-H thymidine was used.

[0094] Tables 5 and 6 provide the concentration for the coumermycin control and compounds, as well as the proliferation results and number of wells/row (n) of the microplate.

5TABLE 5Proliferation of STAT5b-GyrB Transfected BAF Cells FollowingStimulation with Coumermycin or Coumermycin Analogs2371Conc.Prolif.456Prolif.89Compound(graph)(cpm)S.D.nCompound(cpm)S.D. 2NDMSO0.09616142421DMSO616142421Cou. 9000.9606336711Cmpd 2 900601434410pMpMCou. 99675067411Cmpd 2 9603132612nMnMCou. 9090759543710Cmpd 2 90662324111nMnMCou. 450450845753011Cmpd 2 450751345012nMnMCou. 900900863660711Cmpd 2 900779846311nMnMCou. 1.81800861055311Cmpd 2 1.8782534312uMμMIL-21828568112IL-21828568112

[0095]

6

TABLE 6

3

1
2
Conc.
4
5
6

Compound
Inhibitor
(graph)
Prolif.
S.D.
n

Cou. 90 nM
DMSO
0.9
7595
437
10

Cou. 90 nM
Cmpd 1 9 nM
9
7713
328
12

Cou. 90 nM
Cmpd 1 90
90
7683
297
11

nM

Cou. 90 nM
Cmpd 1 900
900
7597
209
11

nM

Cou. 90 nM
Cmpd 1 1800
1800
7271
273
10

nM

Cou. 90 nM
DMSO
0.9
7595
437
10

Cou. 90 nM
Cmpd 2
9
7654
182
12

Cou. 90 nM
Cmpd 2
90
7316
391
11

Cou. 90 nM
Cmpd 2
900
8068
434
11

Cou. 90 nM
Cmpd 2
1800
8165
467
11

Example 5

[0096] In this example, Compounds 1 and 2 were compared to 2 comparative novenamime compounds Comparative Compounds 3 and 4, for cell proliferation. The novenamime compounds are as follows:

[0097] The procedure for preparing the compounds, coumermycin controls, as well as the addition of BAF cells and 3-H thymidine were performed in accordance with the Example 4, above.

[0098] Table 7 provides the concentration for the coumermycin control and compounds, as well as the proliferation results and number of wells/row (n) of the microplate.

7TABLE 7Proliferation of STAT5b-GyrB Transfected BAF Cells FollowingStimulation with Coumermycin or Coumermycin Analogs2371Conc.Prolif.456Prolif.89Compound(graph)(cpm)S.D.nCompound(cpm)S.D. 2NDMSO0.0933562294755DMSO33562294755Cou. 900 pM0.936503329212Cmpd 2 90036052245711Cou. 9 nM944455405911Cmpd 2 938236369312nMCou. 90 nM9051248511612Cmpd 2 9042674350312nMCou. 450 nM45060293546512Cmpd 2 45047023408512nMCou. 900 nM90064831650712Cmpd 2 90046989312912nMCou 1.8 μM180068728375312Cmpd 2 1.846345334412μMIL-2131314938260IL-2131314938260DMSO0.0933562294755DMSO33562294755CCmpd 40.935624325212Cmpd 1 90031865214612900 pMpMCCmpd 4 9935985430812Cmpd 1 934279279512nMnMCCmpd 4 909036764245111Cmpd 1 9033933275212nMnMCCmpd 445036763325812Cmpd 1 45035212261312450 nMnMCCmpd 490035379345211Cmpd 1 90033301253012900 nMnMCCmpd 4180031918278811Cmpd 1 1.8310292035121.8 μMμMIL-2IL-2131314938260DMSO0.0933562294755CCmpd 30.932299304512900 pMCCmpd 3 9933921298512nMCCmpd 3 909033671400111nMCCmpd 345033712220512450 nMCCmpd 390031968303212900 nMCCmpd 31800284341564111.8 μMIL-2131314938260

Coumermycin analogs as chemical dimerizers of chimeric proteins

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