SOLID PHASE SYNTHESIS OF HETEROCYCLIC COMPOUNDS AND COMBINATORIAL COMPOUND LIBRARY
The synthesis of combinatorial compound libraries is rapidly taking on the role of a powerful component within modern lead finding processes that aim at the identification of compounds with novel target activities of interest. In the drug discovery context, the ability to synthesize small organic molecules with high yield on a solid support has a definite strategic relevance. It facilitates the preparation of compound arrays in multiple parallel syntheses and enables the application of combinatorial methods for the synthesis of large libraries suitable for systematic evaluations in biochemical or biological test systems. In view of the expected biostability and bioavailabihty, small organics (e. g. heterocycles) rather than chain-like bioohgomers are more attractive leads for subsequent medicinal chemistry efforts.
Here we report a scope and limitation study on a reaction sequence on solid phase, suitable for the generation of molecular diversity on small heterocycles of the pyrazole and isoxazole type. For each reaction, suitable conditions on solid phase were worked out and a variety of reactive agents (building blocks) was utilized in an effort to grasp the system's breadth of applicability. The inventive reaction sequence can be applied, for example, to exploit by the combinatorial approaches of the split and mix concept. Surprisingly, using the inventive method a new facile way for the synthesis of combinatorial compound libraries consisting of modified heterocyclic rings in high yields and purity is provided. These combinatorial compound libraries serve as valuable reservoirs for the screening for pharmaceutically active compounds.
Detailed description of the invention
The current invention concerns a solid phase synthesis of a heterocyclic ring, characterized in that it comprises the following steps:
a) a solid carrier having reactive surface groups is loaded directely or via a spacer group with a compound bearing an acetyl function,
b) said acetyl function is modified using the Claisen condensation,
c) optional the reaction product of step b) is modified with an α-alkylation step, and d) the heterocyclic ring is closed using a compound comprising two nucleophiles, wherein at least one of said nucleophiles is NH2.
In a preferred embodiment of the invention
step a) is of formula 1
wherein
Z is a solid carrier;
R1 is a substituted or unsubstituted conjugated system that has no acidic hydrogen atoms; and
R
5 is hydrogen, C
1-C
6alkyl, C
1-C
6alkylaryl, C
1-C
6alkoxy-C
1-C
6alkyl, C
1-C
6alkoxycarbonyl- C
1-C
6alkyl; each of which may be substituted or unsubstituted; step b) is of formula 2
wherein
Z, R1 and R5 are defined as above;
R2 is substituted or unsubstituted C1 -C6alkyl, or a substituted or unsubstituted aromatic or aliphatic ring; and
R4 is C1 -C6alkyl, preferred is methyl and ethyl; the optional step c) is of formula 3
wherein
Z, R1, R2 and R4 are defined as above;
R5 is hydrogen
X is a halogen, preferred is I, Br or Cl; and
R3 is C1-C6alkyl, C1-C6alkenyl, C1-C6alkylcarbonyl-C1-C6alkylene, arylcarbonyl-C1- C6alkylene, or a substituted or unsubstituted aromatic or aliphatic ring; and
step d) is of formula 4
wherein
Z, X, R1, R2, R3, R4 and R5 are defined as above,
Y is a nucleophilic center like NH, NC1-C4alkyl, Naryl and O; preferred are O, NH, NC1- C4alkyl, NC1-C4alkyl aryl, Naryl unsubstituted or substituted with up to four Br, Cl, I, F, C1- C4alkyl, NO2, SO2C1-C4alkyl, OC1-Calkyl, carboxy or carbonyl groups, suitable aryl groups are for example thienylene, thiantrenylene, furylene, phenoxanthiinylene, isobenzofuranylene, pyrazolylene, isothiazolylene, isoxazolylene, pyridinylene pyrazinylene, pyrimidylene, indolizinylene, indazolylene, isoquinolylene, quinolylene phthalazinylene, naphthyridinylene, quinoxalinylene, quinazolylene, cinnolinylene, phenylene, naphthylene,
with the proviso that either R3 or R5 is hydrogen.
In a preferred embodiment of the invention the solid carrier Z is a resin. Usually Z is a particle that is insoluble in the reaction media and to which the ligand can be bound in sufficient amount by means of reactive groups at the surface of the this particle.
The binding of ligand and tag is effected, e.g. by amino, carboxyl, hydroxyl or halogen groups. These reactive groups are usually already constituents of the solid carrier, but they can also be applied or modified subsequently. The solid carrier customarily employed in solid-phase synthesis can be used, for example those used in Merrifield peptide synthesis. They consist largely of a polystyrene molecule that is crosslinked by copolymerization with divinyl benzene. The molecules are additionally derivatised to attach the reactants in the solid-phase synthesis.
In a more preferred embodiment of the invention R1 is ethinylene, thienylene, thiantrenylene, furylene, phenoxanthiinylene, isobenzofuranylene, pyrazolylene, isothiazolylene, isoxazolylene, pyridinylene, pyrazinylene, pyrimidylene, indolizinylene, indazolylene, isoquinolylene, quinolylene, phthalazinylene, naphthyridinylene, quinoxalinylene, quinazolyl
ene, cinnolinylene, phenylene, naphthylene,
,
,or
; wherein these conjugated systems are unsubstituted or substituted by groups that have no acidic hydrogens. Suitable groups are, for example, Cl, Br, I, CN, phenyl and pyridyl-groups. Especially preferred R
1 are benzene,
, and
A preferred R2 is, for example ethinyl, thienyl, thiantrenyl, furyl, phenoxanthiinyl, isobenzo- furanyl, pyrazolyl, isothiazolyl, isoxazolyl, pyridinyl, pyrazinyl, pyrimidyl, indolizinyl, indazolyl, isoquinolyl, quinolyl, phthalazinyl, naphthyridinyl, quinoxalinyl, quinazolyl, cinnolinyl, phenyl and naphthyl; wherein these conjugated systems are unsubstituted or substituted by groups that have no acidic hydrogens. Especially preferred is phenyl, 4-CH3OC6H4, 4-ClC6H3(2CI), 4-CH3OOCC6H4, 4-NCC6H4, furyl, pyrrolyl, thienyl, pyridyl, methyl pyrridyl, pyrazinyl, C6H5COOCH3, C6F5, C6H4C(CH3)3, C6H4OCF3, C6H4OCH2C6H5, C6H4O,(CH2)15CH3, C6H3(CF3)2, C6H4O(CH2)3CH3, C6H4CI, C6H4CN, naphthyl, C6H4N(CH3)2, C6H4C6H5, C6H4OCH3, C6H4C6H4COOCH3, C6H2(OCH3)3, C6H3Cl2,
A preferred R3 is, for example, hydrogen, C1-C6alkyl, C1-C4alkoxy-C1-C4alkyl, C1-C6alkenyl, C1-C4alkoxy-aryl, C1-C5alkanoyloxy-C1-C6alkyl, C1-C6alkoxycarbonyl-C1-C5alkyl. Especially preferred is hydrogen, ethyl, NCCH2, CH3CH2OOCCH2, C6H5COCH2 and CH2=CHCH2.
The inventive solid phase synthesis can be used for the generation of combinatorial compound libraries, e.g., in a the split and mix concept (Furka et al., Abstr. 14th Int. Congr. Biochem., Prague (1988), 5, 47; Furka et al., Int. J. Peptide Protein Res. (1991), 37, 487).
For example, in the first step the solid support is loaded with the R1 component bearing the acetyl function (see table 1). Its carbonyl group is activated by standard methods and anchored to the acid labile Rink amide linker on polystyrene (Rink, Tetrahedron Lett. (1987), 28, 3787). We observe quantitative transformations within 1 hour, unless ortho substituted
bifunctional derivatives like o-acetophenone and acetylphthalanilidic acid are used, which undergo ring closure side reactions (Nishio et al., Heterocycl. Chem. (1995), 32, 883).
For the Claisen condensation, optimization of the reaction protocol with the prototypic aromatic ester ethyl benzoate identified conditions, which ensure that also deactivated benzoates and heteroaromatic carboxylic esters condense without appreciable formation of side products (see table 2). As expected, carboxylic esters with α-hydrogens (2g) are unsuited, and also weakly acidic heteroaromatic compounds (2k) cannot be applied. The same is the case for nitro derivatives which are prone to reduction. Noticeably, the series of successful conversions to the diketone included a deactivated ester (2b), as well as a bifunctional building block and a component with an additional electrophilic center (2e and 2f resp.).
With regards to the α-alkylation step, we obtain best results in the presence of TBAF, which has the function to shield the oxygen atoms of the β-dicarbonyl intermediate, hence inhibiting O-alkylation as a side reaction and furthermore increasing the nucleophilicity of the compound. Water traces are detrimental to the yield, which otherwise lies around 90% of the C-monoalkylated product. To expand the diversity, alkylating agents other than the simple alkyl iodides described in analogous solution chemistry can be used (Clark et al., J. Chem Soc, Perkin Trans. I (1977), 1743). Ethyl bromoacetate and allyl bromide react without side reactions. With iodoacetonitrile 35% of starting material is observed and bromoacetophenone does not convert cleanly. The failure with benzyl bromide is rather unexpected. The alkylation step is incompatible with the presence of acid or basic heteroaromatic R1 and R2 residues: with the phenyl pyridine diketone 2j several side products are observed upon alkylation with all the listed alkylating agents. Naturally, dispensing with the alkylation altogether enables to broaden the choice of building blocks for the previous Claisen condensation by allowing e.g. the inclusion of N-heterocyclic esters as an alternative source of diversity.
Ring closure to form a heterocyclic scaffold is tested successfully with hydrazines 4a-d and hydroxylamine (5a) (see table 4). With the non-alkylated intermediate 2a a faster cyclization kinetics than with 3a is observed. N-mono-substituted reagents are expected to yield regioisomers with equal efficiency, unless the intermediates would bear large differences of steric and electronic properties at the R1 and R2 sites.
During the validation process we isolate both regioisomers of model compound 4d. In this instance we intentionally explore the limits by choosing a difficult case, since hydralazine (for electronic and stenc reasons) is predicted to have a relatively weak tendency to cyclize In fact, after 1 day, only traces of the regioisomers 4d are detectable, and it takes 4 days to obtain a level of 20 % conversion, in the presence of the unsubstituted analog 4a originating from the far more reactive impurity 2a (the non-alkylated diketone precursor).
The collected data on the conversion rates of a variety of reactants within our proposed synthetic scheme provide an information basis sufficient for the planning of combinatorial libraries along different lines of strategies. Decisions can be made on which types of building blocks to include for diversity generation and whether to skip a reaction step in favor of a broader choice of compatible residues or simplified reaction conditions . Moreover, the general utility of the approach could be exploited to form additional ring types (e.g pyrimidines from amidines see formula 5) if the diketone intermediates were subjected to cyclization with other reagents bearing two nucleophilic centers.
General method for the synthesis:
a) Loading of a solid carrier with an acetyl function
4-(2',4'-Dimethoxyphenyl-fmoc-aminomethyl)phenoxy resin (Rink amide resin) is subjected to repeated ishes with 20% piperidine/DMF until no UV absorption from Fmoc is detected in the eluate. b) Coupling procedure:
The NH2-linker group is acylated with 0.3 M-solution of acetyl carboxylic acid (3 eq) at RT (preactivation 40 min with 3.3 eq DICD and 3.3 eq HOBt) until the Kaiser test (Kaiser et al., Anal. Biochem. (1970), 34, 595) is negative.
c) Claisen condensation
50 mg (22.5 μmol) of the modified resin are suspended in a solution of 675 μmol carboxylic ester in 670 μl DMA. Under inert gas 18 mg (450 μmol) of sodium hydride (60% dispersion in mineral oil) is added and the reaction mixture is well shaken for 1h at 90 °C. The resin is filtered, ished (30% v/v acetic acid / H2O, DMA, DMSO, and i-propanole), and dried under reduced pressure. d) α-Alkylation step (if necessary)
20 mg (8.6 μmol) of this modified resin is treated with 86 μl 1M TBAF in THF for 2h at room temperature. After addition of 150 μl of a 2.5 M solution of the appropriate alkylating agent, the reaction is continued for another 2 h. The resin is filtered off and ished well with CH2Cl2 and THF. e) Ring closure
The resin resulting from these modifications is heated with 500 μl of a 2.5 M solution of hydrazine derivatives or hydroxyl amine (HCl is neutralized by N(CH3CH2)3) in DMA for 24 h at 80°C. f) Release of the compound from the solid carrier
Cleavage from the support is done by with 20% v/v TFA/CH2Cl2 (Rink, Tetrahedron Lett (1987), 28, 3787).
A suitable method for the preparation of a combinatorial compound library comprises, for example, the reaction steps as described above, wherein optionally before a reaction step is carried out,
a) the resin pool is divided into different portions,
b) said reaction step is carried out in each portion using a different chemical compound or reaction, and
c) the portions are mixed together.
Alos embraced by the scope of the current invention is the combinatorial compound library obtainable by the method described above.
In order to synthesize a combinatorial compound library, e.g. according to Houghten et al. Nature (1991) 354, 84-86; a solid carrier having reactive surface groups is loaded with a compound bearing an acetyl function; or the resin is divided first into several portions then loaded with a different compound bearing an acetyl function in each portion and mixed again. Afterwards, e.g. , the pool containing the modified resin is divided into several separate portions again. The Claisen condensation is carried out in each portion using a different reagent to get different compounds. These separated pools are mixed and, if appropriate, divided again into several separate portions in which the optional α-alkylation step using different reagents is carried out and, afterwards, the separated pools are mixed again. If desired, the mixture may be divided into several separate portions again for carrying out the ring closure with a different agent in each portion. After mixing, a combinatorial compound library has been created that is suitable, e.g., for screening.
Abbreviations
Examples
The products that are produced in each step are analyzed after cleavage from the solid carrier by the following method:
Cleavage from the support is done by with 20% v/v TFA/CH2Cl2 (Rink, Tetrahedron Lett. (1987), 28, 3787).
HPLC analytical separation is achieved using a reverse phase nucleosil C18 5μ 250 mm × 4.6 mm column, 215 nm, 10-90% CH3CN / 0.1% TFA over 30 mm, 1 ml/min.
A part of the eluate (split 1 :25) is introduced into a Quattro-BQ mass spectrometer (VG Biotech, Altnncham, England), operating at a source temperature of 60°C and a cone voltage of 50 V, via an electrospray interface (EI). The mass range from 100 to 800 Dalton is scanned in 4 seconds.
Example 1 Loading of the resin with a compound bearing an acetyl function
Deprotection: 4-(2',4'-Dimethoxyphenyl-fmoc-aminomethyl)phenoxy resin (Rink amide resin) is subjected to repeated washes with 20% piperidine/DMF until no UV absorption from Fmoc is detected in the eluate.
Coupling procedure: The NH
2-linker group is acylated with 0.3 M-solution of 3 eq of a compound of formula 6
at RT (preactivation 40 min with 3.3 eq DICD and 3.3 eq HOBt) until the Kaiser test (Kaiser, E. et al. Anal. Biochem. 1970, 34, 595) is negative . The loading of the resin is 424 μmol/g.
Example 2 Alternative loading of the resin
Deprotection 4-(2',4'-Dimethoxyphenyl-fmoc-aminomethyl)phenoxy resin (Rink amide resin) is subjected to repeated washes with 20% piperidine/DMF until no UV absorption from Fmoc is detected in the eluate.
Coupling procedure: The NH2-linker group is acylated with 0.3 M-solution of 3 eq of a compound of formula 7
at RT (preactivation 40 min with 3.3 eq DICD and 3.3 eq HOBt) until the Kaiser test (Kaiser, E. et al. Anal Biochem 1970, 34, 595) is negative. The loading of the resin is 410 (resin capacity in [μmol/g]).
Example 3 : Claisen condensations
50 mg (22.5 μmol) the modified resin of example 1 are suspended in a solution of 675 μmol carboxylic ester in 670 μl DMA (see table 5). Under inert gas 18 mg (450 μmol) of sodium hydride (60%) is added and the reaction mixture is well shaken for 1h at 90 °C. The resin is filtered, ished (30% v/v acetic acid / H
2O, DMA, DMSO, and i-propanole), and dried under reduced pressure.
Example 4 : Heterocyclic compounds with two or three substituents
50 mg (22.5 μmol) modified resin of example 1 are suspended in a solution of 675 μmol methylbenzoate in 670 μl DMA. Under inert gas 18 mg (450 μmol) of sodium hydride (60%) is added and the reaction mixture is well shaken for 1h at 90 °C. The resin is filtered, ished (30% v/v acetic acid / H2O, DMA, DMSO, and i-PrOH), and dried under reduced pressure to give a compound of formula 9.
This modified resin is heated with 500 μl of a 2.5 M solution of a nucleophile (HCl is neutralized by N(CH
3CH
2)
3) in DMA for 20-24 h (see table 6) to give the desired heterocyclic products (see table 6).
The products have been analyzed using HPLC after cleavage from the resin as described above
Example 5 Heterocyclic compounds with four substituents
50 mg (22.5 μmol) modified resin of example 1 are suspended in a solution of 675 μmol methylbenzoate in 670 μl DMA. Under inert gas 18 mg (450 μmol) of sodium hydride (60%) is added and the reaction mixture is well shaken for 1h at 90 °C. The resin is filtered, ished (30% v/v acetic acid / H2O, DMA, DMSO, and i-propanole), and dried under reduced pressure. 20 mg (8.6 μmol) of this modified resin is treated with 86 μl 1 M TBAF in THF for 2h at room temperature. After addition of 150 μl of a 2.5 M solution of the appropriate alkylating agent (see table 7), the reaction is continued for another 2 h. The resin is filtered off and ished well with CH2Cl2 and THF. Than the modified resin is heated with 500 μl of a
50 % solution of methylhydrazine (HCl is neutralized by N(CH3CH2)3) in ethanol for 16 h at 56°C to give the desired heterocyclic products (see table 7).
The products have been analyzed using HPLC after cleavage from the resin as described above.
Example 6 : Ring closure with compound that has a weak tendency to cyclize
Deprotection 4-(2',4'-Dimethoxyphenyl-aminomethyl)phenoxy resin (Rink amide resin) is subjected to repeated washes with 20% piperidine/DMF until no UV absorption from Fmoc is detected in the eluate.
The NH
2-linker group of 1.50 g 4-(2',4'-Dimethoxyphenyl-fmoc-aminomethyl)phenoxy resin (Rink amide resin) is acylated with a 0.3 M-solution of a compound of formula 10 (3 eq) at RT (after preactivation for 40 mm with 3.3 eq DICD and 3.3 eq HOBt) until the Kaiser test (Kaiser, E. et al. Anal. Biochem 1970, 34, 595) is negative to form a compound of formula 11.
A portion of the product is cleaved from the resin as defined above and analyzed:
100% purity by HPLC, 10.2 min, MS (El) m/z 163 (M+).
50 mg (22.5 μmot) of the compound of formula 11 are suspended in a solution of 0.51g (3.4 mmol) C6H5COOCH2CH3 in 670 μl DMA. Under inert gas 0.14 g (3.4 mmol) NaH (60% dispersion in mineral oil), and 10.5 ml DMA ;and the reaction mixture is well shaken for 1h at 90 °C. The resin is filtered, ished (30% v/v acetic acid / H2O, DMA, DMSO, and i-propanole), and dried under reduced pressure to get a compound of formula 12.
A portion of the product is cleaved from the resin as defined above and analyzed
95% purity by HPLC, 26.3 mm, MS (El) m/z 267 (M+).
20 mg (8.6 μmol) of this resin is treated with 86 μl 1M TBAF in THF for 2h at room temperature. After addition of 150 μl of a 2.5 M of CH3CH2l in CH2Cl2, the reaction is continued for another 2 h. The resin is filtered off and ished well with CH2Cl2 and THF to give a compound of formula 13.
A portion of the product is cleaved from the resin as defined above and analyzed.
75% purity by HPLC, 22.7 min, MS (El) m/z 294 (M+).
The compounds of formulas 13 is heated for 4 days under reflux with 1.09 g (6 75 mmol) hydralazine and 67 mg (0.67 mmol) acetylacetone in CH3CH2OH to form of the two isomeres of formulas 14 and 15.
For analyzation the product is cleaved from the resin with 20% v/v TFA/CH2Cl2 as defined above.
HPLC preparative separation is achieved using a reverse phase nucleosil C18 5μ 20 mm ×
250 mm column, 215 nm, 10-90% CH3CN/0. 1% TFA over 90 mm, 15 ml/mm (10% purity by
HPLC, 25.3 mm for isomer 15 and 26.3 mm for isomer 14) isomer 15:
1H-NMR (DMSO-d
6) δ 9.72 (s, 1H), 8.29 (m, 1H), 8.11 (m, 4H), 8.02 (d, J = 8.6 Hz, 2H), 7.90 (d, J = 8 6 Hz, 2H) 7.46 (bs, 1H), 7.32 (m, 2H), 7.24 (m, 1H), 2.77 (q, J = 7.4 Hz, 2H), 1.06 (t, J = 7 4 Hz, 3H), MS (El) m/z 420 (M
+). isomer 14:
1H-NMR (DMSO-d
6) δ 9.71 (s, 1H), 8 29 (m, 1H), 8.20 (m, 1H), 8.15 (m, 2H), 7.99 (bs, 1H), 7.82 (m, 4H), 7.51 (m, 4H), 7.42 (bs, 1H), 7.31 (d, J = 8 5 Hz, 2H), MS (El) m/z 420 (M
+).
Example 7 : Pyrazole/Isoxazole library
In a first step the acetyl carboxylic acids Ra 1 to Ra 4 are coupled to the resin in separate vessels. The four portions are mixed and distributed in 35 vessels, where each portion reacted with a distinct Rc reagent, a carboxylic acid ester. The result is a randomized Ra and a fixed Rc position. The beads are mixed again and divided into 42 equal portions, of which 41 are reacted with monosubstituted hydrazines Re. We get a pyrazole library with 11480 compounds divided into 41 sublibraries with 280 compounds each. The remaining last portion of the beads is reacted with hydroxylamme to an isoxazole library comprising 280 compounds. The reagents are used are defined below.
Library Synthesis
Coupling of 4 acetyl carboxylic acids to Rink amide resin: Four portions, of Rink amide resin each 0.5 g (208.5 μmol) are treated with 3 eq of a 0.3 M solution of the appropriate carboxylic acid (agent for Ra) which is preactivated with 3.3 eq DICD and HOBt for 40 minutes. After the Kaiser test is negative the four portions are mixed and washed with DMA, DMSO, and i-PrOH and dried under vacuo .
Claisen Condensation: The resin from the former coupling procedure is divided in 35 separate reaction vessels. Under inert gas atmosphere 21 mg (521 μmol) sodium hydride and 782 μmol carboxylic acid ester (agent for Rc)in 770 μl DMA are added to each resin portion (23 4 μmol). The vigorously mixed reaction mixtures are heated 75 mm at 90°C. All portions are mixed and washed with 30 % v/v acetic acid/water, THF, DMA, DMSO, i-PrOH and dried under vacuo.
Cyclization: 1.6 g (640 μmol) are separated in 42 reaction vessels and each resin is treated with 790 μl of a 0.5 M solution of the appropriate monosubstituted hydrazine in DMA (agent for Re). After heating the reaction mixtures for 3 days at 90°C each portion is washed separately with DMA, DMSO , and i-PrOH.
Cleavage Approx. 1/3 of the library material, i. e . 12.07 mg (5 μmol) resin from each sublibrary are mixed with 300 μl 20 % v/v TFA/CH2Cl2 three times for 30 minutes. Then the resin is washed with 300 μl 1 ,2-dichloroethane and 300 μl trifluoroethanol. The solvents are evaporated in a microcentrifuge and the residue is dissolved in 500 μl DMSO .