Patent Application
20080096907
The present invention relates to certain substituted aryl pyrimidyl compounds and to a process for their synthesis. It also relates to pharmaceutical compositions comprising them and to their use as antimicrobial agents, especially for the prevention or treatment of pathologies in relationship with a mycobacteria.
The invention relates in particular to the use of such molecules for the prevention or treatment of tuberculosis and other diseases caused by a mycobacteria.
The incidence of tuberculosis has been increasing during the last twenty years and it is now the first cause of mortality among infectious diseases in the world, killing more than two million people a year. Mycobacterium tuberculosis (M. tuberculosis) is the principal microbial agent involved for humans. Tuberculosis is primarily transmitted via airborne aerosoled secretions. A peculiar aspect of its pathogenicity comes from the fact that it can remain quiescent and become active decades later. One of the most significant risk factor for developing tuberculosis is human immunodeficiency virus (HIV) infection. The current treatment of active tuberculosis includes four drugs (isoniazid, rifampicin, pyrazinamide and ethambutol) for at least six months. A significant proportion of patients do not complete the therapy, especially in developing countries, and this has led to the appearance of resistant strains of M. tuberculosis.
Consequently, there is a need for new molecules which are efficient against M. tuberculosis.
In this context thymidine monophosphate kinase (TMPK), one essential enzyme of nucleotide metabolism is an interesting target.
TMPK (E.C.2.7.4.9, ATP:TMP phosphotransferase) belongs to a large superfamily of nucleoside monophosphate kinases (NMPK). It catalyses the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phosphoryl donor. It lies at the junction of the de novo and salvage pathways of thymidine triphosphate (TTP) metabolism and is the last specific enzyme for its synthesis. These characteristics make TMPK a good target for the design of new antibiotic drugs.
Purine and pyrimidine nucleoside analogues acting on the TMPK of M. tuberculosis have been disclosed in S. Pochet et al., Chem. Bio. Chem. 2003, 4, 742-747.
However there is always a need for molecules with a stronger biological activity, a better specificity, an improved bioavailability, and molecules which would be easier to synthesize, so that their production on industrial scale can be envisioned.
An object of the instant invention is the molecules responding to formula (I):
wherein:
Alkyl is a linear, branched or cyclic hydrogeno carbon radical.
Alkenyl is a linear, branched or cyclic hydrocarbyl radical comprising at least one double bond.
Alkynyl is a linear, branched or cyclic hydrocarbyl radical comprising at least one triple bond.
Halogen is selected from the group consisting of Cl, F, Br, I.
When the alkyl, alkenyl or alkynyl chain is interrupted by a heteroatom this heteroatom may be divalent or trivalent. In this last case, the heteroatom may be substituted by an alkyl, alkenyl or alkynyl group, which itself may possibly be substituted with one of the functions: —OH, —NH2, —CHO, —COOH, —SO4H, —CONH2, —CN, —COOR5, —COR5, —OR5 or a halogen atom.
Preferentially, the molecule responding to formula (I) satisfies one or more of the following conditions.
More preferentially, R2═R3═H.
Advantageously R4 is in the para position on the phenyl ring.
In a preferred manner, R4 is selected from the group consisting of substituted C1-C6 alkyl or substituted C2-C6 alkenyl, wherein the substituent is —COOH, possibly comprising a heteroatom bridge, said heteroatom being selected from: N, S, O, Se.
Even more preferentially R4 is selected from the group consisting of C2-C4 alkyl substituted by one —COOH, or a C1-C8 alkyl interrupted by a sulphur bridge.
Advantageously, R4 is 4-yl-n-butyric acid
The favourite molecules are described by their chemical formula here-under:
The above described molecules have demonstrated their capacity to inhibit M. tuberculosis TMPK and consequently they can be used for the preparation of a medicament for the prevention and/or treatment of tuberculosis. It must be said that these molecules have a capacity to inhibit M. tuberculosis TMPK in vitro which varies in Ki value, according to which molecule is concerned. However, the inhibitory activity exists and permits to have good hopes of an in vivo inhibition of M. tuberculosis TMPK. Preferred molecules are the ones whose Ki is inferior or equal to 40 μM, and even more preferentially inferior or equal to 30 μM. The molecules 20, 21, 22, 39, 61, 63 and 64 depicted here-above are the favourite molecules for their action as inhibitors of M. tuberculosis TMPK.
The molecules of the invention can also be used as an inhibitor of a mycobacteria TMPK, especially M. tuberculosis TMPK in vitro, for biological tests for example.
Moreover, these molecules can also be used for the preparation of a medicament for the prevention or treatment of other pathologies caused by a mycobacteria, among which: leprosy (M. leprae).
The compounds of the instant invention have the advantage of having a lower affinity for human TMPK than for M. tuberculosis TMPK. Consequently, side effects of a drug based on these compounds administered at therapeutic dosage would be limited.
The instant invention encompasses pharmaceutical compositions comprising at least one compound of formula (I) in a pharmaceutically acceptable carrier. The routes of administration include the oral, buccal, intranasal, ocular, intraveneous, intramuscular, transdermal, parenteral and rectal routes. Preferentially when the pathology to be treated is tuberculosis, the pharmaceutical composition of the invention is administered by oral or intranasal route as tablets, pills, dragees, capsules, gels, suspensions, syrups. It may be distributed in an aerosol or as solution for inhalation or any other form which allows easy volatilization for rapid administration to the lung.
The dosage and posology of the pharmaceutical composition is adapted to the weight, age and condition of the patient and to the inhibitory action of the molecule. The daily dose of active principle is comprised between 0,1 and 500 mg/kg.
Pharmaceutically acceptable salts encompass salts of acid functions of (I) with an organic or an inorganic base and salts of an amine function of (I) with an organic or mineral acid.
Among addition salts with acids are included: acetic, oxalic, succinic, fumaric, gluconic, malic, ascorbic, benzoic, hydrochloric, phosphoric, hydrobromic, sulphuric, sulfinic, formic, toluene sulfonic, methane sulfonic, nitric, benzoic, citric, tartaric, maleic, hydroiodic salts.
Among addition salts with bases are included: sodium, potassium and lithium salts; calcium, barium and magnesium salts; ammonium, ferrous, ferric, zinc, manganese, aluminium, magnesium salts; trimethylamine, triethylamine, tri(n-propyl)amine, dicyclohexylamine, triethanolamine, arginine, lysine, histidine, ethylenediamine, glucosamine, methylglucamine, purines, piperazines, piperidines, caffeine, procaine salts.
Pharmaceutically acceptable carriers can include one or several of the following compounds in a non limitating manner: fillers, such as sugar, starch, gelatine, gum, cellulose derivatives (methyl cellulose, hydroxy propylmethyl cellulose), polyvinylpyrrolidone, agar, alginic acid, talc, polyethylene glycol, pharmaceutically acceptable pigments and dyes, stabilizers, oils, liquid paraffin, ethanol, glycerids.
Preparation of Molecules
Another object of the instant invention is a process for the synthesis of the molecules of formula (I).
This process can be described by scheme 1 here-under:
According to the process of the instant invention a haloaryl of formula (II) is reacted with a thymine or thymine derivative or uracyle or uracyle derivative of formula (III) to give the condensate (IV). In formula (II): X represents a halogen atom, preferentially Br; X2, X3, X4 are selected among R2, R3 and R4 respectively and their chemical precursors. In formula (III) and in formula (IV), X1 is selected among R1 and its chemical precursors, X5 is selected among H and the benzyl group (Bzl).
By chemical precursors (X1, X2, X3 and X4) is meant a functional group which can be transformed in one or more steps into the desired functional group (R1, R2, R3 and R4).
As an example, if R1 is H, or halogen, then X1 is respectively H or said halogen, but if R1 is —CH2—COOH, then X1 can be —CH2—COOBz1, or —CH2—OH, or —CH2—Br, so that the alkylation of the thymine cycle can be effected in the absence of any side reaction.
In a second step and if necessary, X1, X2, X3, X4 and X5 are transformed into R1, R2, R3, R4 and H respectively to give the molecule of formula (I).
According to a favourite variant of the invention, R2═R3═H and R6═CH2. Then a key intermediate molecule for the synthesis of the molecules of formula (I) is:
wherein X1 and X5 have the same definition as explained above.
And especially in the case when R1 is CH3, favourite intermediate molecules (V) for the preparation of other molecules of formula (I) are:
The use of a compound of formula (V), and especially compounds 11 and 11bis for the preparation of a molecule responding to formula (I) is another object of the invention.
The above-explained strategy is illustrated in the examples and in the schemes 2 and 3 here-under.
Favourite synthetic routes are based upon Heck or Sonogashira C—C palladium-catalysed coupling reactions between an aryl halide and a suitable alkene or alkyne (Scheme 4). Typically, the first step is the arylation of thymine or uracyle (N1-benzoylated). Starting from this key halide intermediate (IV), various commercially available acids, esters or alcohols (depending on the selected chain length) were coupled using the Heck or Sonogashira reaction.
We considered for the preparation of N1-benzyl thymine substituted by a C3 arm, the Heck palladium-catalyzed coupling reaction (Palladium-catalyzed reactions of organic halides with olefins, R. F. Heck et al, Accounts of Chemical Research, (1979), 12(4), 146-151) of an aryl bromide or iodide with an olefin as a precursor of the C3 chain (Scheme 5). Starting from the commercially available 4-iodo-benzyl bromide, N3-benzoylthymine was first alkylated to give 23 (88% yield) and then debenzoylated into iodide 24 (95% yield). A mixture of 24 and ethyl acrylate in anhydrous acetonitrile in the presence of Pd(OAc)2 (2%), tri-o-toluoylphosphine (4%) and triethylamine was stirred at 90° C. for 18 h. The trans-olefin 17 was isolated in 97% yield. Compound 17 allowed the obtention of the target molecules 1 and 2, and also served as a precursor for the synthesis of three other related derivatives (14, 18, 19). Thus, hydrogenation on 10% Pd/C of the acrylic ethyl ester 17 afforded the propionic ethyl ester 19 (91% yield). Treatment of 19 in 1N NaOH afforded the propionic acid 2 (59% yield), while treatment of 19 in 35% aqueous ammonia gave the target compound 1 (90% yield). In the same manner, saponification of 17 afforded the propenacid derivative 18, while ammonolysis of 17 afforded the propenamide 14 in similar yields.
The synthesis of N1-benzyl-thymine substituted in para by a C4 chain was depicted in Scheme 5. Two routes were investigated in accordance with the precursor chosen for introducing the carboxylic acid function. To obtain compound 20 according to the Heck-coupling reaction, a mixture of 24 and 3-butenoic acid in the presence of Pd(OAc)2 (2%), tri-o-toluoylphosphine (4%) in acetonitrile and triethylamine was heated at 60° C. Olefin 28 was isolated in 27% yield while iodide 24 was recovered. Only one stereoisomer (Z-3, 4) was isolated as confirmed by NMR analysis. Raising the temperature to 90° C. did not improve the yield. When arylation was conducted starting from iodide 23, the coupling yield was slightly improved due to a facilitated purification of the corresponding resulting N1-benzoylated derivative 28 (39%). The alkene 28 was then reduced with H2 on 10% Pd—C to give C4 acid 20 (97% yield). Alternatively, compound 20 was obtained by the C—C coupling of 24 and a commercially available alkyne (Sonogashira reaction). Thus, but-3-yn-1-ol and iodide 24 in the presence of tetrakis(triphenylphosphine)palladium (6%), copper(I) iodide (2%) was refluxed at 90° C. in a mixture of CH2Cl2 and Et3N under argon for 72 h. Compound 30 was isolated as the major arylation product in 40% yield. When the arylation was conducted at 60° C. for 72 h, 30 was isolated in 49% yield. Alkynol 30 was then reduced with H2 on 10% Pd—C to give alcohol 31 (98% yield). Oxidation with PDC in the presence of t-butanol, followed by acid hydrolysis of the intermediate t-butyl ester gave the C4 acid 20 (46% yield in two steps). Reaction of acid 20 in refluxing methanol in the presence of Dowex H+ followed by treatment of the resulting methyl ester 40a with ammonia in methanol afforded amide 40b (58% yield in two steps).
For the synthesis of uracyl derivatives, the same sequences were followed starting from 4-halogenobenzyl-uracyle. Thus, Heck coupling reaction of iodide 25 (obtained by alkylation of N1-benzoyluracyle with 4-iodobenzyl bromide) and methyl 3-butynoate afforded methyl ester 29a in 42% yield. Saponification of 29a gave acid 29b, while catalytic hydrogenation of 29a and saponification afforded acid 38a. Alternatively, Sonogashira coupling of bromide 11 and but-3-yn-1-ol afforded alkyne 36 in good yield (64%). Catalytic reduction into alcohol 37, oxidation into t-butyl ester followed by acid hydrolysis gave uracyl acid derivative 38a (49% yield in three steps). Bromation and chloration of 38a afforded the corresponding 5-Br and 5-Cl derivatives, 21 (70% yield) and 39 (49% yield), respectively. Conversion of acid 38b via methyl ester 38a into amide 41 was followed by bromation or chloration to yield 5-bromo or 5-chloro uracyl derivative 42 and 43, respectively.
N1-benzyl-thymine having a C5 chain ended with a carboxylic acid was obtained in two steps by coupling an aryl halide and a suitable C5 alkyne (Scheme 6). Heck reaction between bromide 11 and 4-pentenoic acid in the presence of Pd(OAc)2 and tri-o-toluoylphosphine gave 44 in 48% yield as a mixture of three stereoisomers: 4-E-pentenoic acid (44a), 3-E-pentenoic acid (44b) and 2-E-pentenoic acid (44c) in a ratio of 5/2/1 according to NMR analysis. Starting from N3-benzoylated thymine bromide 11bis, the coupling reaction was slightly improved (63% yield) while the purification of the products was enhanced. After debenzoylation, 44 was obtained in a similar overall yield. Reduction of the isomeric mixture of olefins 44 yielded the saturated C5 acid 45 (55% yield). Similarly, N1-benzyl-uracyle substituted with a C5 chain was obtained by using Heck coupling of N3-benzoylated uracyl iodide 25 and 4-pentenoic acid (61%), followed by debenzoylation and catalytic hydrogenation of olefins 46 afforded acid 47, which was brominated and chlorinated to give 5-bromo and 5-chloro derivatives 48 and 49, respectively.
N-benzyl-thymine and 5-halogenated uracyle with a C6 chain were obtained by using the palladium-catalyzed Sonogashira reaction between an iodide and a suitable C6 alkyne ended with a carboxylic acid or alcohol. An example of each synthetic route is depicted in Scheme 7. In order to facilitate the purification of the arylation products, we started from the key intermediate 23 or 25 (when bases were N1-benzoylated). Thus, the palladium-catalyzed Sonogashira reaction between 23 and 5-hexynoic acid in the presence of tetrakis(triphenylphosphine)palladium (6%), copper(I) iodide (2%) gave 50 in 80% yield. Debenzoylation of 50 into 51, followed by hydrogenation resulted into saturated C6 acid 22 (50% yield in two steps). Conversion of acid 51 into amide 53 via the corresponding methyl ester 52, followed by reduction of 53 afforded C6 spacer amide 54 (42% yield in two steps). When 5-hexyn-1-ol was coupled with iodide 25, compound 55 was obtained in 70% yield. Debenzoylation followed by hydrogenation gave C6 alcohol 56 (83%). Chromic oxidation of 56 afforded C6 acid 57, which was brominated and chlorinated to give 5-bromo and 5-chloro-uracyl derivatives 58 and 59, respectively. Similarly, 5-halogenated uracyl derivatives ended with a C6 amide 61 and 62 were synthesized from amide 60 (obtained from acide 57).
General information Solvents were spectroscopic or HPLC grade. Reagents were purchased from Sigma-Aldrich or Fluka and used without purification. 1H and 13C NMR spectra were recorded on a Bruker AC-400 spectrometer, operating at 400.13 MHz and 100.62 MHz, respectively. Chemical shifts are given in ppm (δ) relative to residual solvent peak for 1H and 13C, coupling constants (J) are reported in Hertz, and the normal abbreviations are used. Thin layer chromatography (TLC) was performed using Merck silica gel plates (Kieselgel 60 F254/0.2 mm thickness) and spots were visualised by UV light, then revealed by sulfuric acid-anisaldehyde spray followed by heating. Column chromatography was performed with Merck silica gel 60 (230-400 mesh). Preparative HPLC were carried out on a Perkin Elmer system (200 Pump) with a C18 reverse phase column (Kromasil, 5100 Å, 150×4.5 mm) using a flow rate of 5.5 ml/min and a linear gradient of CH3CN (A) in 10 mM triethylammonium acetate buffer (B) at pH 7.5 over 20 min. Eluted products were visualized using a diode array detector. Purity of compounds was checked by anaytical HPLC on a C18 reverse phase column using a flow rate of 1 ml/min. ESI-TOF mass spectra were recorded by the mass spectroscopy laboratory (CNRS-ICSN, Gif-sur-Yvette).
General Procedure for N-alkylation (Scheme 2 and 3)
To a stirred solution of thymine (or related base) (100 mg) in DMF (4 ml) was added anhydrous K2CO3 (100 mg). A solution of aryl halide (1.1 eq.) in DMF (1 ml) was added over a period of 1 h, the stirring was maintained overnight at room temperature. The insoluble was removed by filtration and the filtrate was concentrated to dryness by co-evaporation with xylene. The crude residue was dissolved in CH2Cl2 and washed with water. The organic layer was dried, concentrated under vacuum and purified by column chromatography on silica gel (gradient of methanol in dichloromethane) to give N1, N3-dialkylated and N1-alkylated thymine in a 1:1.2-1.3 ratio.
Alternatively, alkylation of N3-benzoyl-thymine (obtained in two steps from thymine in 74% yield according to the method described in “The Benzoylation of Uracil and Thymine”, Cruickshank, K. A.; Jiricny, J.; Reese, C. B.; (1984) Tet. Letts., 25 (6), 681-684) afforded the N1-alkylated N3-benzoyl-thymine as a unique product in 84% yield. Benzoyl deprotection under basic conditions (33% aqueous ammonia in methanol) results in the corresponding N4-alkylated thymine (nearly quant. yield).
Reaction of thymine (300 mg), K2CO3 (330 mg) with 4-bromo-benzyl bromide (1.1 eq) in DMF (15 ml) yielded after purification compound 11 (302 mg, 43% yield). 1H NMR (CDCl3) δ: 1.96 (d, 3H, CH3, J=1.2 Hz), 4.85 (s, 2H, PhCH2), 6.98 (d, 1H, H6, J=1.2 Hz), 7.19 (d, 2H, H arom., J=8 Hz), 7.51 (d, 2H, H arom.), 9.47 (bs, 1H, NH). 13C NMR (CDCl3) δ: 12.76 (CH3), 50.86 (PhCH2), 111.98 (C5), 122.94 (C arom.), 130.07 and 132.63 (CH arom.), 134.93 (C arom.), 139.88 (C6), 151.59 (C2), 164.53 (C4). MS (ESI-TOF) m/z 295.0 and 297.0 (15%, M+H)+, 317.0 and 319.0 (20%, M+Na)+, 339.0 and 341.0 (100%, 85%, M+2Na)+.
Reaction of N3-benzoyl-thymine (230 mg, 1 mmol) with 4-bromo-benzyl bromide (140 mg) yielded after purification compound 11bis (336 mg, 84% yield). 1H NMR (DMSO-d6) δ: 1.85 (d, 3H, CH3, J=1.1 Hz), 4.90 (s, 2H, PhCH2), 7.32 (d, 2H, H arom., J=8.4 Hz), 7.78 (m, 4H, H arom. and H arom. Bz), 7.78 (t, 1H, H arom. Bz), 7.93 (m, 2H, H arom. Bz), 7.95 (d, 1H, H6, J=1.1 Hz). 13C NMR (DMSO-d6) δ: 12.73 (CH3), 51.14 (PhCH2), 110.08 (C5), 121.93 (C arom.), 130.36, 130.71, 131.14 (CH arom.), 131.98 (C arom.), 132.49 and 136.32 (CH arom.), 136.64 (C arom.), 143.04 (C6), 150.38 (C2), 163.69 (C4), 170.46 (COBz). MS (ESI-TOF) m/z 421.0 and 423.0 (100% and 90%, M+Na).
To a solution of compound 11 (1.94 g, 6.57 mmol) in dry CH2Cl2 (10 ml) were added under Ar freshly distilled Et3N (27 ml), 3-butyn-1-ol (0.46 g, 6.57 mmol), tetrakis(triphenylphosphine)palladium (0.45 g, 0.39 mmol) and cuprous iodide (25 mg, 0.13 mmol). The reaction mixture was heated under reflux for 72 h. To the cooled mixture, CH2Cl2 (100 ml) was added and the resulting solution was washed with 5% aqueous citric acid (3×100 ml), then water. The organic layer was dried over Na2SO4, concentrated under vacuo. Purification by silica gel column chromatography (0-10% gradient of methanol in dichloromethane) afforded recovered starting material (0.52 g, 27%), then compound 30 as a white powder (0.44 g, 24%). 1H NMR (DMSO-d6) δ: 1.75 (d, 3H, CH3, J=1.2 Hz), 2.54 (t, 2H, CH2), 3.58 (q, 2H, CH2OH), 4.83 (s, 2H, PhCH2), 4.92 (t, 1H, OH), 7.25 (d, 2H, H arom., J=8 Hz), 7.37 (d, 2H, H arom., J=8 Hz), 7.61 (d, 1H, H6, J=1.2 Hz), 11.33 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 12.77 (CH3), 24.09 (CH2), 50.72 (PhCH2), 60.57 (CH2), 81.54 (C alcyn), 89.68 (C alcyn), 109.98 (C5), 123.32 (C arom.), 128.40 (CH arom.), 132.38 (CH arom.), 137.63 (C arom.), 142.14 (C6), 151.84 (C2), 165.13 (C4). HRMS (ESI-TOF) m/z calculated for C16H17N2O3+Na 307.1059; found 307.1048.
To a solution of compound 30 (0.34 g, 1.19 mmol) in a mixture of CH2Cl2/methanol (1 ml/10 ml) was added Pd/C (100 mg). Hydrogen was applied overnight, then the mixture was passed through celite and the filtrate concentrated to dryness to give 31 after purification by silica gel column chromatography (0-10% gradient of methanol in dichloromethane) (0.24 g, 70% yield). 1H NMR (DMSO-d6) δ: 1.42 (m, 2H, CH2CH2), 1.57 (m, 2H, CH), 1.75 (d, 3H, CH3, J=1.2 Hz), 2.55 (t, 2H, CH2Ph), 3.40 (m, 2H, CH2OH), 4.36 (t, 1H, OH), 4.79 (s, 2H, PhCH2), 7.11 (d, 2H, H arom., J=8.4 Hz), 7.20 (d, 2H, H arom., J=8.4 Hz), 7.61 (d, 1H, H6, J=1.2 Hz), 11.30 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 12.77 (CH3), 28.27 (CH2), 32.93 (CH2), 35.47 (CH2), 50.63 (PhCH2), 61.36 (CH2), 109.83 (C5), 128.29 (C arom.), 129.41 (CH arom.), 135.13 (CH arom.), 142.12 (C6), 142.67 (C arom.), 151.85 (C2), 165.09 (C4). HRMS (ESI-TOF) m/z calculated for C16H20N2O3+Na 311.1372; found 311.1374.
To a stirred solution of compound 31 (80 mg, 0.28 mmol) in dry CH2Cl2 (3 ml) were added t-butanol (0.54 ml, 5.6 mmol), acetic anhydride (0.26 ml, 2.8 mmol) and pyridinium dichromate (0.21 g, 0.56 mmol). After stirring for 1 h 30 at room temperature, starting material was consumed as judged by TLC. The crude mixture was loaded on a silica gel column chromatography conditioned in ethyl acetate, let on the silica gel for 15 min., then eluted with ethyl acetate. The fractions containing the expected ester were pooled, concentrated under vacuo and then treated with 2N NaOH (1 ml) in methanol (5 ml) overnight. The reaction mixture was acidified by addition of cationic resin (Dowex H+) until pH 3, filtered and lyophilized. Purification by reverse phase HPLC (5-30% linear gradient of acetonitrile in buffer, Rt=14 min.) gave compound 20 (20 mg, 25%). 1H NMR (DMSO-d6) δ: 1.75 (d, 3H, CH3, J=1.2 Hz), 1.78 (m, 2H, CH2), 2.20 (t, 2H, CH2), 2.57 (t, 2H, CH2), 4.80 (s, 1H, H5), 7.19 (m, 4H, H arom.), 7.61 (d, 1H, H6, J=1.2 Hz), 11.30 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 12.78 (CH3), 27.12 (CH2), 33.97 (CH2), 34.90 (CH2), 50.61 (PhCH2), 109.83 (C5), 128.37 (CH arom.), 129.44 (CH arom.), 135.37 (C arom.), 141.92 (C arom.), 142.12 (C6), 151.86 (C2), 165.08 (C4), 175.09 (COOH). MS (ESI-TOF) m/z 325.1 (100%, M+Na)+. HRMS (ESI-TOF) m/z calculated for C16H18N2O4+Na 325.1178; found 325.0357.
A suspension of uracil (4.94 g, 44.0 mmol) and potassium carbonate (4.7 g, 33.9 mmol) in anhydrous DMF (60 ml) was stirred at room temperature for 1 h, then 4-bromobenzylmethyl bromide (8.47 g, 33.9 mmol) was added. After stirring overnight, the mixture was purified to give compound 35 (3.15 g, 33% yield). 1H NMR (DMSO-d6) δ: 4.85 (s, 2H, PhCH2), 5.60 (d, 1H, H5, J=7.8 Hz), 7.26 (d, 2H, H arom., J=8.4 Hz), 7.60 (dt, 2H, H arom., J=8.4 Hz, J=2 Hz), 7.76 (d, 1H, H6, J=7.8 Hz), 11.34 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 50.60 (PhCH2), 102.32 (C5), 121.69 (C arom.), 130.58 CH arom.), 132.39 (CH arom.), 137.17 (CH arom.), 146.38 (C6), 151.84 (C2), 164.48 (C4). MS (ESI-TOF) m/z 281.0 and 283.0 (M+H)+, 303.0 and 305.0 (M+Na)+, 325.0 and 327.0 (M+2Na)+, 335.0 and 337.0.
To a solution of compound 35 (1.46 g, 5.21 mmol) in dry CH2Cl2 (40 ml) were added under Ar freshly distilled Et3N (45 ml), 3-butyn-1-ol (0.44 g, 6.57 mmol), tetrakis(triphenylphosphine)palladium (0.37 g, 0.31 mmol) and cuprous iodide (20 mg, 0.10 mmol). The reaction mixture was heated at 80° C. for 90 h and worked up as for compound 30 to give compound 36. 1H NMR (DMSO-d6) δ: 1.19 (t, 21H, CH3), 2.54 (t, 2H, CH2), 3.10 (t, 14H, CH2), 3.57 (q, 2H, CH2), 4.87 (s, 2H, PhCH2), 4.89 (t, 1H, OH), 5.60 (dd, 1H, H5, J=7.8 Hz, J=2.1 Hz), 7.25 (d, 2H, H arom., J=8.3 Hz), 7.38 (dd, 2H, H arom., J=6.5 Hz, J=2.7 Hz), 7.76 (d, 1H, H6), 9.10 (bs, 2.3H, NH), 11.33 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 24.12 (CH2), 50.88 (PhCH2), 60.56 (CH2), 81.52 (C alcyn), 89.72 (C alcyn), 102.26 (C5), 123.36 (C arom.), 128.41 (CH arom.), 132.38 (CH arom.), 137.50 (C arom.), 146.38 (C6), 151.85 (C2), 164.50 (C4). MS (ESI-TOF) m/z 293.1 (100%, M+Na)+, 333.2 (5%, M+Na+ K)+.
Compound 36 (0.55 g, 2.0 mmol) was hydrogenated as for compound 30 to give after purification compound 37 (0.25 g, 46%). 1H NMR (DMSO-d6) δ: 1.41 (m, 2H, CH2), 1.57 (m, 2H, CH2), 2.55 (t, 2H, CH2), 3.39 (m, 2H, CH2), 4.35 (t, 1H, OH), 4.83 (s, 2H, PhCH2), 5.58 (dd, 1H, H5, J=7.8 Hz, J=2.3 Hz), 7.19 (m, 4H, H arom.), 7.74 (d, 1H, H6, J=7.8 Hz), 11.30 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 28.26 (CH2), 32.93 (CH2), 35.46 (CH2), 50.84 (PhCH2), 61.34 (CH2OH), 102.14 (C5), 128.40 (CH arom.), 129.42 (CH arom.), 134.95 (C arom.), 142.74 (C arom.), 146.45 (C6), 151.86 (C2), 164.50 (C4). MS (ESI-TOF) m/z 297.1 (100%, M+Na)+, 431.4 (40%).
4-[4-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-ylmethyl)-phenyl]-butyric acid (38b) Compound 38b was obtained in two steps: chromic oxidation of compound 37 (135 mg, 0.5 mmol) as described for compound 32 gave the corresponding t-butyl ester (125 mg, 70%). Saponification of the ester (105 mg, 0.29 mmol) afforded compound 38b as a white powder (68 mg, 80%). 1H NMR (DMSO-d6) δ: 1.77 (m, 2H, CH2), 2.21 (t, 2H, CH2), 2.57 (t, 2H, CH2), 4.83 (s, 2H, PhCH2), 5.58 (dd, 1H, H5, J=2.2 Hz and J=7.8 Hz), 7.20 (m, 4H, H arom.), 7.74 (d, 1H, H6, J=8.8 Hz), 11.30 (bs, 1H, NH), 12.05 (bs, 1H, COOH). 13C NMR (DMSO-d6) δ: 27.08 (CH2), 33.91 (CH2), 34.89 (CH2), 50.83 (PhCH2), 102.15 (C5), 128.40 (CH arom.), 129.46 (CH arom.), 135.19 (C arom.), 141.97 (C arom.), 146.44 (C6), 151.86 (C2), 164.50 (C4), 175.04 (COOH). HRMS (ESI-TOF) m/z calculated for C15H16N2O4+Na 311.1008; found 311.1022.
To compound 38b (50 mg, 0.17 mmol) in pyridine (3 ml) was added a 1M solution of bromine in CCl4 (0.23 ml). After stirring for 1 h30 reaction was complete, the solution was concentrated under vacuo. Purification by silica gel column chromatography (0-20% gradient of methanol in dichloromethane) afforded compound 21 as a pale yellow powder (45 mg, 70%). 1H NMR (DMSO-d6) δ: 1.77 (m, 2H, CH2), 2.21 (t, 2H, CH2, J=7.3 Hz), 2.57 (t, 2H, CH2), 4.84 (s, 2H, PhCH2), 7.18 (d, 2H, H arom., J=8.1 Hz), 7.25 (d, 2H, H arom.), 8.35 (d, 1H, H6), 11.83 (bs, 1H, NH), 12.05 (bs, 1H, COOH). 13C NMR (DMSO-d6) δ: 27.08 (CH2), 33.92 (CH2), 34.90 (CH2), 51.32 (PhCH2), 95.92 (C5), 128.51 (CH arom.), 129.45 (CH arom.), 134.84 (C arom.), 142.09 (C arom.), 146.02 (C6), 151.22 (C2), 160.44 (C4), 175.04 (COOH). MS (ESI-TOF) m/z 389.0 (100%, M+Na)+, 391.0 (86%, M+Na)+. HRMS (ESI-TOF) m/z calculated for C11H15N2O479Br+Na 389.0113 and C15H15N2O481Br+Na 391.0092; found 389.0140 (100%) and 391.0136 (87%).
Reaction of thymine with benzyl bromide yielded after purification compound 3 (57 mg, % yield). 1H NMR (CDCl3) δ: 1.90 (d, 3H, CH3, J=1.1 Hz), 4.92 (s, 2H, PhCH2), 7.00 (d, 1H, H6, J=1.1 Hz), 7.31 (m, 2H, H arom.), 7.39 (m, 3H, H arom.), 9.14 (bs, 1H, NH). MS (ESI-TOF) m/z 217.1 (60%, M+H)+, 239.1 (100%, M+Na)+.
Reaction of 5-bromo-uracil with benzyl bromide yielded after purification compound 4. 1H NMR (CDCl3) δ: 4.91 (s, 2H, PhCH2), 7.30-7.40 (m, 5H, H arom.), 8.37 (s, 1H, H6), 11.84 (bs, 1H, NH).
Reaction of 5-fluoro-uracil with benzyl bromide yielded after purification compound 5. 1H NMR (DMSO-d6) δ: 4.89 (s, 2H, PhCH2), 7.34 (m, 5H, H arom.), 8.37 (s, 1H, H6), 11.84 (bs, 1H, NH). MS (ESI-TOF) m/z 279 (M+2Na).
Reaction of thymine with 4-fluoro-benzyl chloride yielded after purification compound 6 (64 mg, 35% yield). 1H NMR (CDCl3) δ: 1.89 (d, 3H, CH3, J=1.1 Hz), 4.87 (s, 2H, PhCH2), 6.99 (d, 1H, H6, J=1.1 Hz), 7.06 (m, 2H, H arom.), 7.30 (m, 2H, H arom.), 9.75 (bs, 1H, NH). 13C NMR (CDCl3) δ: 12.75 (CH3), 50.76 (PhCH2), 111.87 (C5), 116.18 and 116.52 (CH arom.), 130.25 and 130.33 (CH arom.), 131.78 and 131.81 (C arom.), 139.95 (C6), 151.73 (C2), 161.84 and 161.30 (C arom.), 164.74 (C4). MS (ESI-TOF) m/z 235.1 (90%, M+H)+, 257.1 (40%, M+Na)+, 279.1 (50%, M+2Na)+.
Reaction of thymine with 3-fluoro-benzyl chloride yielded after purification compound 7 (48 mg, 26% yield). 1H NMR (CDCl3) δ: 1.90 (d, 3H, CH3, J=1.1 Hz), 4.90 (s, 2H, PhCH2), 7.05 (m, 3H, H6 and H arom.), 7.08 (d, 1H, H arom.), 7.35 (m, 1H, H arom.), 9.75 (bs, 1H, NH). 13C NMR (CDCl3) δ: 12.75 (CH3), 50.86 (PhCH2), 111.98 (C5), 115.18 and 115.40 (CH arom.), 115.69 and 115.90 (CH arom.), 123.83 and 123.86 (CH arom.), 131.06 and 131.14 (CH arom.), 138.36 and 138.44 (C arom.), 140.00 (C6), 151.68 (C2), 162.19 (C4), 164.66 and 164.72 (C arom.). MS (ESI-TOF) m/z 235.1 (100%, M+H)+, 257.1 (5%, M+Na)+, 279.1 (70%, M+2Na)+.
Reaction of thymine with 3,4-difluoro-benzyl bromide yielded after purification compound 8 (60 mg, 30% yield). 1H NMR (CDCl3) δ: 1.89 (d, 3H, CH3, J=1.1 Hz), 4.90 (s, 2H, PhCH2), 5.30 (d, 1H, ═CH, J=11 Hz), 5.77 (d, 1H, ═CH, J=18 Hz), 6.72 (dd, 1H, ═CH, J=11 Hz, J=18 Hz), 6.98 (d, 1H, H6, J=1.1 Hz), 7.27 (m, 2H, H arom., J=8 Hz), 7.42 (m, 2H, H arom.), 9.26 (bs, 1H, NH). 13C NMR (CDCl3) δ: 12.74 (CH3), 50.61 (PhCH2), 112.15 (C5), 117.47 and 117.64 (CH arom.), 118.25 and 118.43 (CH arom.), 124.46, 124.49, 124.52 and 124.56 (CH arom.), 132.85 and 132.90 (C arom.), 139.76 (C6), 149.46, 149.58, 149.63 and 149.75 (C arom.), 151.49 (C2), 151.93, 152.06, 152.11 and 152.24 (C arom.), 164.48 (C4). MS (ESI-TOF) m/z 253.1 (100%, M+H)+.
Reaction of thymine with 4-chloro-benzyl chloride (1.1 eq) yielded after purification compound 8 (71 mg, 36% yield). 1H NMR (CDCl3) δ: 1.89 (d, 3H, CH3, J=1 Hz), 4.86 (s, 2H, PbCH2), 6.99 (d, 1H, H6), 7.25 (d, 2H, H arom.), 7.34 (d, 2H, H arom.), 9.88 (bs, 1H, NH). 13C NMR (CDCl3) δ: 12.75 (CH3), 50.80 (PhCH2), 111.96 (C5), 126.65 and 129.77 (CH arom.), 134.44 and 134.82 (C arom.), 139.92 (C6), 151.68 (C2), 164.66 (C4). MS (ESI-TOF) m/z 251.1 (20%, M+H)+, 295.0 (100%, M+2Na)+.
Reaction of thymine with 3-chloro-benzyl chloride (1.1 eq) yielded after purification compound (52 mg, 26% yield). 1H NMR (CDCl3) δ: 1.92 (d, 3H, CH3, J=1.1 Hz), 4.88 (s, 2H, PhCH2), 6.99 (d, 1H, H6, J=1.1 Hz), 7.20 (m, 1H, H arom.), 7.28 (m, 1H, H arom.), 7.32 (m, 2H, H arom.), 9.45 (bs, 1H, NH). 13C NMR (CDCl3) δ: 12.77 (CH3), 50.85 (PhCH2), 112.03 (C5), 126.44, 128.37, 129.06 and 130.79 (CH arom.), 135.36 (C arom.), 137.92 (C6), 139.92 (C arom.), 151.55 (C2), 164.52 (C4). MS (ESI-TOF) m/z 251.1 (100%, M+H)+, 273.0 (25%, M+Na)+, 295.0 (35%, M+2Na)+.
Reaction of thymine (300 mg), K2CO3 (330 mg) with 4-bromobenzyl bromide (1.1 eq) in DMF (15 ml) yielded after purification compound (302 mg, 43% yield).
1H NMR (DMSO-d6) δ: 1.75 (d, 3H, CH3, J=1.2 Hz), 4.81 (s, 2H, PhCH2), 7.26 (d, 2H, H arom., J=8.3 Hz), 7.56 (d, 2H, H arom., J=8.3 Hz), 7.64 (d, 1H, H6, J=1.2 Hz), 11.34 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 12.79 (CH3), 50.37 (PhCH2), 109.99 (C5), 121.63 (C arom.), 130.57 and 132.38 (CH arom.), 137.34 (C arom.), 142.03 (C6), 151.83 (C2), 165.07 (C4). MS (ESI-TOF) m/z 295.0 and 297.0 (15%, M+H)+, 317.0 and 319.0 (20%, M+Na)+, 339.0 and 341.0 (100%, 85%, M+2Na)+.
3-[4-(5-Methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-ylmethyl)-phenyl]-acrylic acid ethyl ester (17). 1H NMR (DMSO-d6) δ: 1.26 (t, 3H, CH3), 1.76 (d, 3H, CH3, J=1.1 Hz), 4.19 (q, 2H, OCH2), 4.86 (s, 2H, PhCH2), 6.62 (d, 1H, ═CH, J=16 Hz), 7.32 (d, 2H, H arom., J=8.1 Hz), 7.63 (d, 1H, ═CH), 7.64 (d, 1H, H6, J=1.1 Hz), 7.71 (d, 2H, H arom.), 11.33 (bs, 1H, NH). 13C NMR (CDCl3) δ: 12.79 (CH3), 15.04 (CH2CH3), 50.72 (PhCH2), 60.97 (OCH2), 109.98 (C5), 119.13 (═CH), 128.75 and 129.49 (CH arom.), 134.26 (C arom.), 140.27 (C arom.), 142.27 (C6), 144.70 (═CH), 151.86 (C2), 165.09 (C4), 167.01 (CO). MS (ESI-TOF) m/z 315.1 (5%, M+H)+, 337.1 (100%, M+Na)+, 359.1 (5%, M+2Na)+.
3-[4-(2,4-Dioxo-3,4-dihydro-2H-pyrimidin-1-yl-methyl)-phenyl]-acrylic acid (18). Compound 17 (50 mg, 0.16 mmol) was treated with NaOH (1.3 eq.) for 1 h. The mixture was passed through a Dowex H+ eluted with water. Compound 18 was isolated as a white powder (27 mg, 59% yield). 1H NMR (DMSO-d6) δ: 1.76 (d, 3H, CH3, J=1.2 Hz), 4.86 (s, 2H, PhCH2), 6.52 (d, 1H, ═CH, J=16 Hz), 7.32 (d, 2H arom., J=8.2 Hz), 7.57 (d, 1H, ═CH), 7.64 (s, 1H, H6), 7.68 (d, 2H, H arom.), 11.34 (bs, 1H, NH), 12.40 (bs, 1H, COOH). 13C NMR (DMSO-d6) δ: 13.96 (CH3), 51.87 (PhCH2), 111.14 (C5), 121.37 (═CH), 129.93 (CH arom.), 130.52 (CH arom.), 135.65 (C arom.), 141.19 (C arom.), 143.28 (C6), 145.42 (═CH), 153.04 (C2), 166.26 (C4), 169.54 (COOH). HRMS (ESI-TOF) 7 m/z calculated for C15H13N2O4 285.0875; found 285.0891.
3-[4-(5-Methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-ylmethyl)-phenyl]-acrylamide (14). 1H NMR (DMSO-d6) δ: 1.76 (d, 3H, CH3, J=1.2 Hz), 4.82 (s, 2H, PhCH2), 6.59 (d, 1H, ═CH, J=16 Hz), 7.09 (bs, 1H, CONH2), 7.32 (d, 2H, H arom., J=8.2 Hz), 7.40 (d, 1H, ═CH), 7.55 (bd, 3H, H arom. and CONH2), 7.64 (s, 1H, H6), 11.32 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 12.79 (CH3), 50.69 (PhCH2), 109.87 (C5), 123.30 (═CH), 127.50 (CH arom.), 128.23, 128.68 and 128.80 (CH arom.), 135.12 (C arom.), 139.18 (C arom.), 139.48 (═CH), 142.12 (C6), 151.86 (C2), 165.09 (C4), 167.45 (CONH2). MS (ESI-TOF) m/z 285.2 (75%) 286.2 (100%, M+H)+, 307.1 308.1 (40%, M+Na)+.
3-[4-(5-Methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-ylmethyl)-phenyl]-propionic acid ethyl ester (19). To compound 17 (90 mg, 0.28 mmol) in methanol (10 ml) was added Pd black (9 mg). Hydrogen was applied overnight, then the mixture was passed through celite and the filtrate concentrated to dryness to give 19 (83 mg, 91% yield). 1H NMR (DMSO-d6) δ: 1.14 (t, 3H, CH3), 1.74 (d, 3H, CH3, J=1 Hz), 2.59 (t, 2H, CH2, J=7.5 Hz), 2.82 (t, 2H, CH2), 4.03 (q, 2H, OCH2, J=7 Hz), 4.79 (s, 2H, PhCH2), 7.20 (bs, 4H, H arom.), 7.60 (d, 1H, H6, J=1.0 Hz), 11.29 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 12.79 (CH3), 14.92 (OCH2CH3), 30.77 (CH2), 35.82 (CH2), 50.59 (PhCH2), 60.67 (OCH2), 109.82 (C5), 128.38 (CH arom.), 129.38 (CH arom.), 135.67 (C arom.), 140.83 (C arom.), 142.06 (C6), 151.92 (C2), 165.17 (C4), 172.97 (COOEt). MS (ESI-TOF) m/z 339.1 (100%, M+Na)+.
3-[4-(5-Methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-ylmethyl)-phenyl]-propionic acid (2). Compound 19 (90 mg, 0.28 mmol) was treated with 0.5 N NaOH (1.3 eq.) for 1 h. The mixture was passed through a Dowex H+ eluted with water. Compound 2 was isolated as a white powder (27 mg, 59% yield). 1H NMR (DMSO-d6) δ: 1.75 (d, 3H, CH3, J=1.0 Hz), 2.47 (t, 2H, CH2), 2.79 (t, 2H, CH2, J=7.7 Hz), 4.70 (s, 2H, PhCH2), 7.15 (d, 4H arom.), 7.65 (d, 1H, H6), 11.30 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 12.77 (CH3), 31.09 (CH2), 36.43 (CH2), 50.58 (PhCH2), 109.84 (C5), 128.34 and 129.37 (CH arom.), 135.45 and 141.48 (C arom.), 142.10 (C6), 151.85 (C2), 165.07 (C4). HRMS (ESI-TOF) m/z calculated for C15H16N2O4+Na 311.1008; found 311.1029.
3-[4-(5-Methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-ylmethyl)-phenyl]-propionamide (1). Compound 19 (70 mg, 0.22 mmol) was treated with 33% aqueous ammonia (25 ml) at room temperature overnight. Purification by silica gel column chromatography (0-8% gradient of methanol in dichloromethane) afforded compound 1 as a white powder (57 mg, 90%). 1H NMR (DMSO-d6) δ: 1.75 (d, 3H, CH3, J=1 Hz), 2.33 (m, 2H, CH2), 2.79 (m, 2H, CH2), 4.79 (s, 1H, H5), 6.74 (bs, 1H, CONH2), 7.20 (m, 4H, H arom.), 7.28 (bs, 1H, CONH2), 7.60 (d, 1H, H6, J=1 Hz), 11.29 (bs, 1H, NH). 13C NMR (DMSO-d6) X: 12.77 (CH3), 31.25 (CH2), 37.41 (CH2), 50.59 (PhCH2), 109.83 (C5), 128.33 (CH arom.), 129.33 (CH arom.), 135.37 (C arom.), 141.82 (C arom.), 142.09 (C6), 151.85 (C2), 165.07 (C4), 174.18 (CONH2). MS (ESI-TOF) m/z 310.1 (100%, M+Na)+. HRMS (MALDI-TOF) m/z calculated for C15H17N3O3+Na 310.1168; found 310.1174.
To compound 38b (50 mg, 0.17 mmol) in pyridine (3 ml) was added a 1M solution of bromine in CCl4 (0.23 ml). After stirring for 1 h30 reaction was complete, the solution was concentrated under vacuo. Purification by silica gel column chromatography (0-20% gradient of methanol in dichloromethane) afforded compound 21 as a pale yellow powder (45 mg, 70%). 1H NMR (DMSO-d6) δ: 1.77 (m, 2H, CH2), 2.21 (t, 2H, CH2, J=7.3 Hz), 2.57 (t, 2H, CH2), 4.84 (s, 2H, PhCH2), 7.18 (d, 2H, H arom., J=8.1 Hz), 7.25 (d, 2H, H arom.), 8.35 (d, 1H, H6), 11.83 (bs, 1H, NH), 12.05 (bs, 1H, COOH). 13C NMR (DMSO-d6) δ: 27.08 (CH2), 33.92 (CH2), 34.90 (CH2), 51.32 (PhCH2), 95.92 (C5), 128.51 (CH arom.), 129.45 (CH arom.), 134.84 (C arom.), 142.09 (C arom.), 146.02 (C6), 151.22 (C2), 160.44 (C4), 175.04 (COOH). MS (ESI-TOF) m/z 389.0 (100%, M+Na)+, 391.0 (86%, M+Na)+. HRMS (ESI-TOF) m/z calculated for C15H15N2O479Br+Na 389.0113 and C15H15N2O481Br+Na 391.0092; found 389.0140 (100%) and 391.0136 (87%).
5-[5-Chloro-4-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl-methyl)-phenyl]-butyric acid (39) 1H NMR (DMSO-d6) δ: 1.77 (m, 2H, CH2), 2.21 (t, 2H, CH2, J=7.4 Hz), 2.57 (t, 2H, CH2, J=7.7 Hz), 4.84 (s, 2H, PhCH2), 7.15 (d, 2H, H arom., J=8.1 Hz), 7.25 (d, 2H, H arom., J=8.1 Hz), 8.29 (s, 1H, H6), 11.89 (bs, 11H, NH). 13C NMR (DMSO-d6) δ: 27.09 (CH2), 33.92 (CH2), 34.90 (CH2), 51.37 (PhCH2), 107.42 (C5), 128.49, 128.51 and 129.46 (CH arom.), 134.78 (C arom.), 142.10 (C arom.), 143.67 (C6), 150.99 (C2), 160.28 (C4), 175.05 (COOH). HRMS (ESI-TOF) m/z calculated for C15H15N2O435Cl+Na 321.0642; found 321.0638 (100%).
4-(5-Bromo-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-ylmethyl)-butyric acid amide (42) 1H NMR (DMSO-d6) δ: 1.76 (m, 2H, CH2), 2.05 (t, 2H, CH2, J=7.5 Hz), 2.54 (t, 2H, CH2, J=7.8 Hz), 4.84 (s, 2H, PhCH2), 6.71 (bs, 1H, CONH2), 7.18 (d, 2H, H arom., J=8.1 Hz), 7.24 (bs, 1H, CONH2), 7.25 (d, 2H, H arom.), 8.36 (s, 1H, H6), 11.83 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 27.63 (CH2), 35.18 (CH2), 35.36 (CH2), 51.32 (PhCH2), 95.93 (C5), 128.49 (CH arom.), 129.46 (CH arom.), 134.76 (C arom.), 142.37 (C arom.), 146.01 (C6), 151.24 (C2), 160.47 (C4), 174.79 (CONH2). HRMS (ESI-TOF) m/z calculated for C15H16N3O379Br+Na 389.0113 and C15H16N3O381Br+Na 390.0252; found 388.0299 (100%) and 390.0282 (83%).
4-(5-Chloro-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-ylmethyl)-butyric acid amide (43) 1H NMR (DMSO-d6) δ: 1.76 (m, 2H, CH2), 2.05 (t, 2H, CH2, J=7.4 Hz), 2.54 (t, 2H, CH2, J=7.7 Hz), 4.84 (s, 2H, PhCH2), 6.71 (bs, 1H, CONH2), 7.18 (d, 2H, H arom., J=8.1 Hz), 7.24 (bs, 1H, CONH2), 7.25 (d, 2H, H arom.), 8.29 (s, 1H, H6), 11.86 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 27.63 (CH2), 35.18 (CH2), 35.36 (CH2), 51.37 (PhCH2), 107.41 (C5), 128.49 (CH arom.), 129.46 (CH arom.), 134.69 (C arom.), 142.37 (C arom.), 143.67 (C6), 151.00 (C2), 160.28 (C4), 174.79 (CONH2). HRMS (ESI-TOF) m/z calculated for C15H15N2O435Cl+Na 344.0778 and C15H15N2O437Cl+ Na 346.0748; found 344.0798 (100%) and 346.0798 (40%).
HRMS (ESI-TOF) m/z calculated for C16H16N2O4+Na 323.1008; found 232.1044.
5-[4-(5-Methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl-methyl)-phenyl]-pentanoic acid (45) 1H NMR (CDCl3) δ: 1.67 (m, 4H, 2×CH2), 1.90 (d, 3H, CH3, J=1.1 Hz), 2.35 (t, 2H, CH2, J=7.1 Hz), 2.65 (t, 2H, CH2, J=7.1 Hz), 4.87 (s, 2H, PhCH2), 6.99 (d, 1H, H6, J=1.2 Hz), 7.21 (m, 4H, H arom.), 8.74 (bs, 1H, NH). 13C NMR (CDCl3) δ: 12.77 (CH3), 24.90 (CH2), 31.11 (CH2), 34.26 (CH2), 35.60 (CH2), 51.12 (PhCH2), 111.52 (C5), 128.47, 128.55 and 129.50 (CH arom.), 133.26 (C arom.), 140.15 (C arom.), 142.95 (C6), 151.42 (C2), 164.31 (C4), 174.39 (COOH). HRMS (ESI-TOF) m/z calculated for C18H22N2O4+Na 353.1477; found 353.1463.
1H NMR (DMSO-d6) δ: 1.52 (m, 4H, 2×CH2), 2.22 (t, 2H, CH2, J=7.1 Hz), 2.56 (t, 2H, CH2, J=7.2 Hz), 4.83 (s, 2H, PhCH2), 5.59 (d, 1H, H5, J=7.8 Hz), 7.20 (m, 4H, H arom.), 7.74 (d, 1H, H6, J=7.8 Hz), 11.31 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 24.98 (CH2), 31.32 (CH2), 34.37 (CH2), 35.30 (CH2), 50.83 (PhCH2), 102.15 (C5), 128.34, 129.18 and 129.41 (CH arom.), 135.02 (C arom.), 142.42 (C arom.), 146.44 (C6), 151.87 (C2), 164.50 (C4), 175.28 (COOH).
5-[4-(5-Bromo-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl-methyl)-phenyl]-pentanoic acid (48) 1H NMR (DMSO-d6) δ: 1.52 (m, 4H, 2×CH2), 2.20 (t, 2H, CH2, J=7.1 Hz), 2.56 (t, 2H, CH2, J=7.2 Hz), 4.84 (s, 2H, PhCH2), 7.19 (d, 2H, H arom.), 7.23 (d, 2H, H arom.), 8.35 (s, 1H, H6), 11.62 (bs, 1H, NH). 13C NMR (DMSO-d6) δ: 25.07 (CH2), 31.25 (CH2), 34.58 (CH2), 35.33 (CH2), 51.31 (PhCH2), 95.93 (C5), 128.45 and 129.51 (CH arom.), 134.68 (C arom.), 142.58 (C arom.), 146.00 (C6), 151.25 (C2), 160.48 (C4), 175.43 (COOH). HRMS (ESI-TOF) m/z calculated for C16H17N2O479Br+Na 403.0269; found 403.0302.
HRMS (ESI-TOF) m/z calculated for C18H18N2O4+Na 349.1164; found 349.1160.
HRMS (ESI-TOF) m/z calculated for C18H19N3O3+Na 348.1324; found 348.1292.
13C NMR (DMSO-d6) δ: 12.78 (CH3), 25.19 (CH2), 29.08 (CH2), 31.55 (CH2), 34.50 (CH2), 35.51 (CH2), 50.62 (PhCH2), 109.81 (C5), 128.31 (CH arom.), 129.39 (CH arom.), 135.15 (C arom.), 142.13 (C6), 142.56 (C arom.), 151.84 (C2), 165.07 (C4), 175.33 (COOH). HRMS (ESI-TOF) m/z calculated for calculated for C18H22N3O4+Na 353.1477; found 353.1455.
13C NMR (DMSO-d6) δ: 12.78 (CH3), 25.77 (CH2), 29.19 (CH2), 31.60 (CH2), 35.54 (CH2), 35.88 (CH2), 50.63 (PhCH2), 109.81 (C5), 128.30 (CH arom.), 129.39 (CH arom.), 135.14 (C arom.), 142.15 (C6), 142.62 (C arom.), 151.85 (C2), 165.08 (C4), 175.11 (CONH2). HRMS (ESI-TOF) m/z calculated for calculated for C18H23N3O3+Na 352.1637; found 352.1601.
1H NMR (DMSO) δ: 1.27 (m, 2H, CH2(c)), 1.52 (m, 4H, 2×CH2 (b and d), 2.19 (t, 2H, CH2 (a), J=6.3 Hz), 2.53 (t, 2H, CH2 (e), J=7.8 Hz and J=7.5 Hz), 4.84 (s, 2H, PhCH2), 7.18 (d, 2H, H arom (x), J=8.2 Hz), 7.24 (d, 2H, H arom (y), J=8.2 Hz), 8.35 (s, 1H, H6), 11.83 (bs, 1H, NH), 11,97 (bs, 1H, COOH). 13C NMR (DMSO-d6) δ: 25.17 (CH2(b)), 29.06 (CH2(c)), 31.52 (CH2(d)), 34.44 (CH2(a)), 35.52 (CH2(e)), 51.33 (CH2(Bz)), 95.90 (C—Br), 128.45 (2×CH(y)), 129.41 (2×CH(x)), 134.62 (Cq(e)), 142.76 (Cq), 146.02 (C6), 151.22 (C2), 160.44 (C4), 175.29 (COOH).
HRMS (ESI-TOF) m/z calculated for C17H19N2O479Br+Na 417.0426; found 417.0443; calculated for C17H19N2O481Br+Na 419.0405; found 419.0412.
1H NMR (DMSO) δ: 1.28 (m, 2H, CH2(c)), 1.52 (m, 4H, 2×CH2 (b and d), 2.21 (t, 2H, CH2 (a), J=7.3 Hz), 2.55 (t, 2H, CH2 (e), J=7.8 Hz and J=7.5 Hz), 4.83 (s, 2H, CH2(Bz)), 7.18 (d, 2H, H arom (x), J=8.1 Hz), 7.24 (d, 2H, H arom (y), J=8.1 Hz), 8.29 (s, 1H, H6), 11.86 (s, 1H, NH), 12.01 (bs, 1H, COOH). 13C NMR (DMSO-d6) δ: 25.17 (CH2(b)), 29.06 (CH2(c)), 31.53 (CH2(d)), 34.44 (CH2(a)), 35.51 (CH2(e)), 51.37 (CH2(Bz)), 107.40 (C—Br), 128.44 (2×CH(y)), 129.41 (2×CH(x)), 134.56 (Cq(e)), 142.76 (Cq(Bz)), 143.67 (C6), 150.99 (C2), 160.27 (C4), 175.29 (COOH). HRMS (ESI-TOF) m/z calculated for C17H19N2O435Cl+Na 373.0931; found 373.0921; calculated for C17H19N2O437Cl+Na 375.0902; found 375.0923.
6-[4-(5-Bromo-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl-methyl)-phenyl]-hexanoic acid amide (61) 1H NMR (DMSO) δ: 1.25 (m, 2H, CH2(c)), 1.51 (m, 4H, 2×CH2 (b and d), 2.04 (t, 2H, CH2 (a), J=7.4 Hz), 2.54 (t, 2H, CH2 (e), J=7.8 Hz and J=7.5 Hz), 4.84 (s, 2H, CH2(Bz)), 6.67 and 7.19 (d, 2H, CONH2, 7.18 (d, 2H, H arom (x), J=8.1 Hz), 7.23 (d, 2H, H arom (y), J=8.1 Hz), 8.35 (s, 1H, H6), 11.82 (s, 1H, NH). 13C NMR (DMSO-d6) δ: 25.77 (CH2(b)), 29.19 (CH2(c)), 31.59 (CH2(d)), 35.55 (CH2(e)), 35.89 (CH2(a)), 51.33 (CH2(Bz)), 95.92 (C—Br), 128.44 (2×CH(y)), 129.41 (2×CH(x)), 134.62 (Cq(e)), 142.81 (Cq(Bz)), 146.00 (C6), 151.24 (C2), 160.47 (C4), 175.09 (CONH2). HRMS (ESI-TOF) m/z calculated for C17H20N3O379Br+Na 416.0586; found 416.0571; calculated for C17H20N3O381Br+Na 418.0565; found 418.0555.
1H NMR (DMSO) δ: 1.25 (m, 2H, CH2(c)), 1.51 (m, 4H, 2×CH2 (b and d), 2.02 (t, 2H, CH2 (a), J=7.4 Hz), 2.54 (t, 2H, CH2 (e), J=7.7 Hz and J=7.5 Hz), 4.83 (s, 2H, CH2(Bz)), 6.67 and 7.19 (each bs, 2H, CONH2), 7.18 (d, 2H, H arom., J=8.2 Hz), 7.24 (d, 2H, H arom., J=8.2 Hz), 8.29 (s, 1H, H6), 11.86 (s, 1H, NH). 13C NMR (DMSO-d6) δ: 25.77 (CH2(b)), 29.19 (CH2(c)), 31.59 (CH2(d)), 34.55 (CH2(e)), 35.89 (CH2(a)), 51.38 (PhCH2), 107.40 (C5), 128.43 (2×CH), 129.41 (2×CH), 134.54 (Cq), 142.81 (Cq), 143.67 (C6), 150.99 (C2), 160.28 (C4), 175.09 (CONH2). HRMS (ESI-TOF) m/z calculated for C17H20N3O335Cl+Na 372.1091; found 372.1093; calculated for C17H20N3O337Cl+Na 374.1061; found 374.1073.
3-[4-(5-Methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-ylmethyl)-benzylsulfanyl]-acetic acid (63). 13C NMR (DMSO-d6) S: 12.79 (CH3), 23.35 (CH2), 33.55 (CH2), 50.60 (PhCH2), 109.89 (C5), 128.38 and 130.08 (CH arom.), 136.63 and 138.08 (C arom.), 142.12 (C6), 151.86 (C2), 165.10 (C4), 172.101 (COOH). HRMS (ESI-TOF) m/z calculated for C15H16N2O4S+Na 343.0728; found 343.0728.
HRMS (ESI-TOF) m/z calculated for C16H17N2O3F+Na 327.1121; found 327.1098.
HRMS (ESI-TOF) m/z calculated for C16H17N2O4F+Na 343.1070; found 343.1052.
Activity was determined using the coupled spectrophotometric assay described in Blondin et al. (C. Blondin, L. Serina, L. Wiesmüller, A. -M. Gilles, O. Bârzu, Anal. Biochem. 1994, 220, 219).
Each mole of transferred phosphoryl group generates two moles of NAD+ and the decrease in absorbance at 334 nm is followed in an Eppendorf ECOM 6122 photometer. The reaction medium (0.5 ml final volume) contained 50 mM Tris-HCl pH 7.4, 50 mM KCl, 2 mM MgCl2, 0.2 mM NADH, 1 mM phosphoenol pyruvate and 2 units each of lactate dehydrogenase, pyruvate kinase and nucleoside diphosphate kinase. One unit of enzyme activity corresponds to 1 μmole of the product formed in 1 min. at 30° C. and pH 7.4. The concentrations of ATP and dTMP were kept constant at 0.5 mM and 0.05 mM respectively, whereas the concentrations of analogues varied between 0.005 and 8 mM. Equation 1 was used to calculate the Ki values using Equations 2 and 3 (classical competitive inhibition model following the Lineweaver-Burk representation):
where v and vi are the reaction velocities respectively in the absence and in the presence of the analogue at a concentration value [I]; Km is the Km for dTMP (4.5 μM for TMPKmt and 5 μM for TMPKh); [S] is the concentration of dTMP (50 μM).
The results are exposed in Table 1 and Table 2:
The IC50 value for three compounds has been measured on cultures of Mycobacterium tuberculosis H37Ra. The results are summarized in Table 3:
Cytotoxicity: The molecule 22 has been tested for its cytotoxicity on VERO cells. It has been determined that no growth inhibition, and consequently no cytotoxic activity, could be detected up to a concentration of 250 μg/ml of compound 22.
| Number | Date | Country | Kind |
|---|---|---|---|
| 04292629.5 | Nov 2004 | EP | regional |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/EP05/12346 | 11/4/2005 | WO | 9/4/2007 |
