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Synthesis and antimicrobial activity of 4-trifluoromethylpyridine nucleosides

  • Shaikha S. Alneyadi , Anas A. Abdulqader , Alaa A. Salem and Ibrahim M. Abdou EMAIL logo
Published/Copyright: April 19, 2017
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Heterocyclic Communications
From the journal Heterocyclic Communications Volume 23 Issue 3

Abstract

4-Trifluoromethylpyridine derivatives 4–8 represent good candidates for the discovery of new antibacterial agents. Fluorinated pyridine nucleosides 4–7 and non-nucleoside analogues 8a,b were synthesized and evaluated for their antibacterial activities against Staphylococcus aureus, Bacillus infantis, Escherichia coli and Stenotrophomonas maltophilia. The minimum inhibitory concentrations (MICs) of the new nucleosides 4–7 range from 1.3 to 4.9 μg/mL and MICs of fluoroaryl derivatives 8a,b are in the range of 1.8–5.5 μg/mL. Activity of amoxicillin, the reference drug, is 1.0–2.0 μg/mL under similar conditions.

Keywords: antimicrobial; fluoropyridine; gHMBC; nucleosides; synthesis

Introduction

The increasing prevalence of life-threatening antibacterial diseases and rapidly growing trend of antimicrobial resistance necessitate the development of new and more effective antimicrobial agents. The 2-pyridones represent a unique class of pharmacophores present in various therapeutic agents [1]. They exhibit antitumor [2], antimalarial [3], analgesic [4] and anti-HIV properties [5] and inhibit in-vitro and in-vivo the bacterial type II DNA topoisomerases, which includes two highly homologous enzymes: DNA gyrase and topoisomerase IV [6]. Fluorine substitution can bring substantial changes in the physical, chemical and biological properties [7] of bioactive molecules.

One important strategy in this respect is chemical synthesis of nucleosides. The use of nucleoside analogues can be considered a novel option as they are expected to act at the genomic level, thereby interfering with the transcription or replication processes required for microbial survival. As there are no alternative pathways in the pathogens for these basic metabolic processes, the nucleoside analogues, by inhibiting these basic pathways, are effective antimicrobial agents [8]. For example, some nucleosides exhibit antibacterial activity by specific inhibition of cell-wall peptidoglycan biosynthesis [9], certain bacterial enzymes, such as purine nucleoside phosphorylases [10] and DNA ligases [11]. Adenosine analogues such as cordycepin [12], oxetanocin [13], formycins [14], toyocamycin and its derivatives [15] show biological activity including antibiotic properties.

Designing expeditious routes to obtain nucleosides is of paramount importance to organic and medicinal chemists. Three general glycosylation methods dominate in nucleoside synthesis. The Fischer approach [16] employs nucleophilic displacement of an α-halogen by the metal salt of a heterocycle to furnish the nucleoside. The fusion method consists of heating a peracylated sugar with a nucleobase. The mildest and most popular method is the Vorbrüggen variant [17, 18] of the Hilbert-Johnson reaction, which makes use of a fully protected sugar and couples it with a silylated nucleobase in the presence of Lewis acids, typically tin tetrachloride (SnCl4) or trimethylsilyl trifluoromethanesulfonate (TMSOTf), among others [19], to provide the protected nucleoside.

In this paper, we describe synthesis of a new class of 4-trifluoromethylpyridine derivatives 4–8. The 4-trifluoromethylpyridine moiety is attached to a sugar moiety (pentose or hexose) in nucleosides 4–7 and to a fluorinated aryl group in analogues 8a,b. These products were evaluated as antibacterial agents.

Results and discussion

Chemistry

3-Cyano-4-trifluoromethyl-6-(thiophen-2′-yl)-2-pyridone 3 was obtained in one-pot condensation of the 1,3-dicarbonyl substrate 1 with equimolar amount of cynoacetamide 2 in refluxing ethanol. The reaction afforded a single product 3 with an 89% yield (Scheme 1). The nuclear magnetic resonance (NMR) spectra of 3 are fully consistent with the assigned structure [20]. The gradient heteronuclear multiple bond correlation (gHMBC) spectrum of 3 (Figure 1) shows a correlation between the signal of thiophene-H3 (δ 8.15) and pyridone-C5 (δ 105.9). The proton signal at δ 8.15 also correlates to the C-6 signal of pyridone-C6 at δ 143.7. Another correlation is observed between the pyridone-H5 signal at δ 7.63 and the signals of C-2′ and C-3′ of the thiophene at δ 129.7 and 140.7, respectively. The gHMBC spectrum does not show any correlation between the thiophene protons and the carbon atom of the CN group at δ 120.5. Based on these observations, the CF3 group must be located at position 4 and the thiophen-2′-yl group at position 6 of the 2-pyridone moiety. The infrared (IR) spectrum of compound 3 shows the most significant absorption band for the amide carbonyl group at 1661 cm−1. A strong band at 2230 cm−1 corresponds to the CN group and a NH signal appears at 3419 cm−1. The UV-vis spectrum of compound 3 (Figure 2) shows two absorption bands at 360 nm and 259 nm. The band at 259 nm can be attributed to the n-σ* transition, while the band at 360 nm is apparently a combination of n-π* and π-π* transitions.

Scheme 1 Reagents and conditions: (a) HMDS, (NH4)2SO4, reflux, 2 h, then 1,2,3,5-tetra-O-acetyl-β-D-ribofuranose, TMSOTf/CH3CN, 0–25°C; (b) TEA/MeOH/H2O; (c) aqueous KOH, 2 h, 2,3,4,6-tetra-O-acetyl-α-D-glucopyranosyl bromide, acetone; (d) TEA/MeOH/H2O; (e) aroyl chloride, pyridine, CH3CN.
Scheme 1

Reagents and conditions: (a) HMDS, (NH4)2SO4, reflux, 2 h, then 1,2,3,5-tetra-O-acetyl-β-D-ribofuranose, TMSOTf/CH3CN, 0–25°C; (b) TEA/MeOH/H2O; (c) aqueous KOH, 2 h, 2,3,4,6-tetra-O-acetyl-α-D-glucopyranosyl bromide, acetone; (d) TEA/MeOH/H2O; (e) aroyl chloride, pyridine, CH3CN.

Figure 1 The gHMBC spectrum in DMSO-d6 of 2-pyridone 3.
Figure 1

The gHMBC spectrum in DMSO-d6 of 2-pyridone 3.

Figure 2 A UV-vis absorption of 3 in 0.01 m Tris–KCl buffer solution, pH 7.4. The buffer was prepared by dissolving 10.0 mm of tris(hydroxymethyl)aminomethane hydrochloride (1.58 g), 1.0 mm Na2EDTA (0.37 g) and 100.0 mm KCl (7.45 g) in 1.0 L of deionized water.
Figure 2

A UV-vis absorption of 3 in 0.01 m Tris–KCl buffer solution, pH 7.4. The buffer was prepared by dissolving 10.0 mm of tris(hydroxymethyl)aminomethane hydrochloride (1.58 g), 1.0 mm Na2EDTA (0.37 g) and 100.0 mm KCl (7.45 g) in 1.0 L of deionized water.

The β-D-ribofuranosyl-2-pyridone 4 was prepared in 68% yield by reaction between a silyl derivative of compound 3 and 1,2,3,5-tetra-O-acetyl-β-D-ribofuranose (Scheme 1). The reaction of a nucleophilic base normally takes place from the less sterically hindered β-face of the intermediate cation to give the β-isomer. The structure of the obtained riboside 4 was confirmed using analytical and spectroscopic data IR, NMR and elemental analysis. The IR spectrum of 4 shows bands at 2215 and 1748 cm−1 indicating the presence of cyano and acetoxy groups, respectively. On the other hand, a sharp peak at 1652 cm−1 for the carbonyl group of the 2-pyridone indicates that the sugar is linked to the pyridine ring through the nitrogen atom giving the N-riboside. In the 1H NMR spectrum of 4, the anomeric proton H-1″ resonates as a doublet at δ 6.41 with a coupling constant JH1″−H2″=4.3 Hz, indicating that the obtained product 4 is a β-isomer. The 13C-NMR spectrum shows a signal at δ 87.2 corresponding to the C-1″ atom of the β-configuration.

The O-glucoside derivative 5 was prepared by the reaction of a potassium salt of 3 with an activated sugar at room temperature. In principle, the ambident 2-pyridone anion contains two reactive nucleophilic centers, the pyridine ring nitrogen and the carbonyl oxygen at C-2. A sole O-nucleoside product has been isolated without the formation of the N-nucleoside. Apparently, α-acetobromoglucose undergoes a reaction with potassium salt of 3 through a Walden inversion, to yield the corresponding glucoside 5. Since Walden inversion occurs in the halogen replacement reaction, the reaction involving halide with the α-configuration yields the β-isomer. The IR spectrum of 5 shows the presence of acetoxy carbonyl groups at 1749 cm−1. A strong band appears at 2231 cm−1 corresponding to the CN group. The 1H-NMR spectrum of 5 shows the β-configuration. The anomeric proton H-1″ appears as a doublet at a relatively low field, δ 6.13. The spin-spin coupling constant, JH1″−H2″=8.0 Hz, indicates that the protons H-1″ and H-2″ are in diaxial orientation. The H-2″ and H-3″ signals appear as a multiplet at δ 5.37–5.45. The H-5″ and H-4″ signals appear as a multiplet at δ 5.15–5.24. The H2-6′,6″ signals appear as a multiplet at δ 4.08–7.11. Protons of the four acetoxy groups appear as four singlets at δ 1.94, 2.03, 2.05 and 2.06. The pyridine H-5 proton resonates at δ 7.62 and this downfield position is consistent with the formation of O-glucoside [20]. The structure of compound 5 was further confirmed by the analysis of the 13C-NMR spectrum which shows a signal at δ 109.7 corresponding to the C-1″ atom of the β-configuration. The signals at δ 154.7 and 141.5 are assigned to C-6 and C-4 of the pyridine ring. Signals at δ 168.8, 169.3, 170.4 and 170.7 belong to the four acetoxy carbonyl carbons. Signals corresponding to pyridine C-5 and C-3 resonate at δ 94.9 and 110.8, respectively. The signals at δ 72.7, 70.0, 68.0, 61.6 and 60.4 can be assigned to C-2″, C-3″, C-4″, C-5″ and C-6″, respectively. On the other hand, the C-2 atom of pyridine appears at δ 162.4 and the signal for the nitrile carbon is observed at δ 119.6.

Deacetylation of 3-cyano-1-(2″,3″,5″-tri-O-acetyl-β-D-ribofuranosyl)-4-trifluoromethyl-6-(thiophen-2′-yl)-2-pyridone 4 afforded nucleoside 6 in 73% yield. The IR absorption spectrum of compound 6 shows a characteristic band at 3428 cm−1 for the sugar hydroxy groups. Another band at 2206 cm−1 can be assigned to the nitrile group. A sharp absorption band at 1655 cm−1 is attributed to the stretching vibration of the carbonyl group of 2-pyridone. In addition, the furanoside ring system shows a broad band at 1050 cm−1. The 1H-NMR spectrum of compound 6 shows a doublet at δ 5.89 corresponding to the anomeric proton of the ribosyl moiety; a coupling constant of 4.0 Hz is consistent with the diaxial orientation of the H-1″ and H-2″ protons and indicates the formation of the β-isomer. The 13C-NMR spectrum of 6 is characterized by a signal at δ 83.5 corresponding to the C1″ atom of the ribosyl residue.

Hydrolysis, to remove the acetyl groups in compound 5 was carried out using triethylamine (TEA) in methanol and produced the free nucleoside 7 in 74% yield. The IR spectrum of 7 shows a characteristic band at 3403 cm−1 due to the sugar four hydroxy groups. Another band at 2206 cm−1 can be assigned to the nitrile group. The IR absorption of ether linkage of the glucopyranoside ring system appears at 1036 cm−1. The 1H NMR spectrum of 7 shows a doublet at δ 7.24 corresponding to the anomeric proton of the glucose moiety. The coupling constant of 8.0 Hz is consistent with the diaxial orientation of the H-1′′ and H-2′′ protons indicating the formation of a single β-isomer. There are four signals corresponding to four hydroxy protons that are exchangeable with D2O. The 13C NMR spectrum of 7 is characterized by a signal at δ 97.3 corresponding to the C-1 atom of the glucose residue.

Non-nucleosides 8a,b were synthesized by the reaction of 3 with an aroyl chloride. This reaction afforded the corresponding products within 30 min in yields of 87% and 85% (Scheme 1). Structures of 8a,b were confirmed by elemental analysis and spectral data. The IR spectrum of 8b shows the presence of one carbonyl group at 1760 cm−1 corresponding to the ester group, which indicates the formation of O-benzoylation product. The band at 1603 cm−1 accounts for the C=C stretch in the aromatic system. The strong band at 2231 cm−1 corresponds to the CN group at C-3. The 1H NMR spectrum contains two doublets at δ 7.95 and 8.35 with coupling constants J=5.0 Hz and 3.7 Hz for the thiophene protons H-5 and H-3 and the resonance for H-4 of the thiophene appears as a triplet at δ 7.29. The H-5 of pyridine resonates in low field at δ 8.55, which confirms the formation of O-benzoylated compound. The 13C NMR spectrum of 8b is also fully consistent with the discussed structure. A similar analysis confirmed the structure of 8a.

Antibacterial properties

An agar-diffusion method was used for the determination of the preliminary antimicrobial activity of compounds 3–8. Amoxicillin was used as a reference drug. The results were recorded for each tested compound as a diameter of an inhibition zone of microbial growth around the disk in mm. The minimum inhibitory concentration (MIC) values were also determined. The inhibition zones (mm) and MIC values (μg/mL) are given in Tables 1 and 2, respectively. As can be seen, the synthesized compounds show good antibacterial activity against all selected bacteria strains with MIC values ranging from 1.3 to 5.5 μg/mL. Compounds 4 and 5 are highly active against S. maltophilia with MIC values of 1.7 and 1.5 μg/mL, respectively. High antibacterial activities of nucleoside 7 (MIC=1.3 μg/mL) and the non-nucleoside derivative 8b (MIC=1.8 μg/mL) against E. coli should be noted.

Table 1

Antibacterial activity of compounds 4–8.

CompoundsZone of inhibition (diameter, mm)
B. infantisE. coliS. aureusS. maltophilia
426281830
532272529
625232423
730292623
8a20201918
8b28312624
Amoxicillin15161514
Table 2

Minimum inhibitory concentration for compounds 4–8.

CompoundsConcentration of compounds (μg/mL) to inhibit 105 cell/mL
B. infantisE. coliS. aureusS. maltophilia
44.32.74.91.7
53.52.32.41.5
64.73.13.02.3
73.81.32.52.0
8a5.53.55.03.6
8b3.21.82.82.8
Amoxicillin11.51.52

Conclusion

Four new pyridine nucleosides 4–7 and two non-nucleoside analogues 8a,b were synthesized. Pyridine ribosides 4, 5 and glucosides 6, 7 are potent antibacterial agents. The antibacterial p-trifluoromethylbenzoate 8b is more active than its p-fluorobenzoate analogue 8a.

Experimental

All reagents and chemicals were purchased from Sigma-Aldrich and used without further purification. Melting points were determined using Pyrex capillaries on a Gallenkamp apparatus. IR spectra were recorded with a Thermo Nicolet Nexus 470 FT-IR spectrometer using KBr disks. 1H NMR (400 MHz) and 13C NMR (100 MHz) spectra were obtained on a Varian Gemini 400 spectrometer in CDCl3 or DMSO-d6. All exchangeable protons were confirmed by addition of D2O. Thin-layer chromatography (TLC) was carried out on Merck silica gel F254 plates and UV light was used for visualization. Column chromatography was performed on a Merck silica gel. Absorption measurements were carried out using an Agilent 8453 spectrophotometer and 1-cm quartz cells. Elemental Analysis was performed on a Leco Model CHN-600 elemental analyzer.

3-Cyano-4-trifluromethyl-6-(thiophen-2′-yl)-2-pyridone (3)

A mixture of 4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione (10.0 mmol, 2.22 g), 2-cyanoacetamide (11.0 mmol, 0.92 g) and potassium hydroxide (12.0 mmol, 0.67 g) in ethanol (50 mL) was heated under reflux for 6 h. The mixture was cooled, acidified with 0.1 m HCl and the resultant precipitate was crystallized from ethanol: yellow powder; yield 89%; mp 293–294°C; IR: 1661 (C=O), 2230 (CN), 3419 cm−1 (NH); 1H NMR (DMSO-d6): δ 7.23 (m, 1H, thiophene-H4), 7.63 (bs, 1H, pyridone-H5), 7.88, 7.89 (dd, 1H, thiophene-H5, J=4.9 Hz), 8.15, 8.16 (dd,1H, thiophene-H3, J=3.7 Hz), 13.57 (bs, 1H, NH, exchangeable with D2O); 13C NMR (DMSO-d6): δ 105.9 (pyridine-C5), 113.8 (pyridine-C3), 120.5 (CN), 129.7–140.5 (aromatic carbons), 143.7 (pyridine-C6), 154.1 (pyridine-C2), 164.8 (pyridine-C4). Anal. Calcd for C11H5F3N2OS: C, 48.89; H, 1.86; N, 10.37; S, 11.87. Found: C, 48.94; H, 1.97; N, 10.28; S, 11.95.

3-Cyano-1-(2″,3″,5″-tri-O-acetyl-β-D-ribofuranosyl)-4-trifluoromethyl-6-(thiophen-2′-yl)-2-pyridone (4)

A mixture of 2-pyridone 3 (0.01 mol, 2.70 g), 1,1,1,3,3,3 hexamethyldisilazane (HMDS, 60 mL), ammonium sulfate (0.0009 mol, 0.125 g) and 2-3 drops of chlorotrimethylsilane was heated under nitrogen for 2 h. Excess HMDS was removed by distillation, and the residue was dried under reduced pressure for 6 h. The resulting silyl intermediate product was dissolved in anhydrous MeCN (20 mL) and a solution of 1″,2″,3″,5″-tetra-O-acetyl-β-D-ribofuranose (0.01 mol, 3.18 g) in 20 mL of MeCN was added with stirring. The mixture was cooled to 5°C, treated with trimethylsilyl trifluoromethanesulfonate (TMSOTf) (0.015 mol, 2.71 mL) and stirred at room temperature for an additional 3 h until the reaction was completed as observed by TLC analysis (ethyl acetate/hexane, 1:1). The mixture was diluted with ethyl acetate (150 mL), and the organic solution was washed with a saturated NaHCO3 solution (50 mL) and then water (2×50 mL). The organic layer was dried with anhydrous Na2SO4, concentrated under a reduced pressure and the residue of 3 was purified by silica gel chromatography using 1% MeOH in ethyl acetate as an eluent to give the pure product as pale brown powder: yield 78%; mp 218°C; IR: 1652 (C=O), 1748 (acetoxy carbonyl), 2215 cm−1 (CN); 1H NMR (CDCl3): δ 2.09, 2.11, 2.12 (3s, 9H, 3CH3), 4.32–4.37 (m, 3H, H-5″a, H-5″b, H-3″), 5.32–5.36 (m, 2H, H-2″, H-4″), 6.41 (d, 1H, H-1″, J=4.3 Hz), 6.85 (s, 1H, pyridine H-5), 7.32 (m, 1H, thiophene-H4), 7.69 (d, 1H, thiophene-H-5, J=5.0 Hz), 8.24 (d, 1H, thiophene-H3, J=3.7 Hz); 13C NMR (DMSO-d6): δ 21.1, 21.2, 21.6 (3CH3), 79.0 (C5″), 79.4 (C3″), 79.7 (C2″), 86.2 (C4″), 87.2 (C1″), 97.2 (pyridine-C5), 111.6 (pyridine-C3), 118.2 (CN), 121.6 (CF3), 124.3 (thiophene-C3), 127.2 (thiophene-C4), 128.7 (thiophene-C5), 130.0 (pyridine-C4), 141.7 (thiophene-C2), 145.3 (pyridine-C6), 155.8 (pyridine-C2), 170.6 (acetoxy carbonyl carbons). Anal. Calcd for C22H19F3N2O8S: C, 50.00; H, 3.62; N, 5.30; S, 6.07. Found: C, 50.09; H, 3.73; N, 5.21; S, 6.87.

3-Cyano-2-(2″,3″,4″,6″-tetra-O-acetyl-β-D-glucopyranosyloxy)-4-trifluoromethyl-6-(thiophen-2′-yl)pyridine (5)

To a solution of 2-pyridone 3 (0.01 mol, 2.70 g) in aqueous KOH (0.01 mol, 0.56 g) in 6.0 mL distilled water, a solution of 2,3,4,6-tetra-O-acetyl-α-D-glycopyranosyl bromide (0.011 mol, 4.11 g) in acetone (30 mL) was added. The mixture was stirred at room temperature until the reaction was judged completed by TLC (4–6 h), then treated with CH2Cl2 (30 mL). The organic layer was dried over Na2SO4, filtered and concentrated under reduced pressure at room temperature. Crystallization of the residue from ethanol gave the nucleoside 5 as pale yellow powder: yield 72%; mp 134°C, IR: 1749 (acetoxy carbonyl), 2231 cm−1 (CN); 1H NMR (CDCl3): δ 1.94, 2.03, 2.05, 2.06 (4s, 12H, 4CH3), 4.08–4.13 (m, 2H, H-6″a, H-6″b), 5.15–5.24 (m, 2H, H-4″, H-5″), 5.37–5.45 (m, 2H, H-2″,H-3″), 6.12, 6.14 (d, 1H, H-1″, J=8.0 Hz), 7.18 (m, 1H, thiophene-H-4), 7.59 (d, 1H, thiophene-H-5, J=5.0 Hz), 7.62 (s, 1H, pyridine H-5), 7.75 (d, 1H, thiophene-H3, J=3.7 Hz); 13C NMR (CDCl3): δ 20.5, 20.6, 20.7, 21.1 (4CH3), 60.4 (C6″), 61.6 (C5″), 68.0 (C4″), 70.0 (C3″), 72.7 (C2″), 94.9 (pyridine-C5), 109.7 (C1″), 110.8 (C3), 119.6 (CN), 122.4 (CF3), 128.9 (thiophene-C3), 129.2 (thiophene-C4), 132.1 (thiophene-C5 ), 141.5 (pyridine-C4), 144.5 (thiophene-C2), 154.7 (pyridine-C6), 162.4 (pyridine-C2), 168.8, 169.3, 170.4, and 170.7 (four acetoxy carbonyl carbon). Anal. Calcd for C25H23F3N2O10S: C, 50.00; H, 3.86; N, 4.66; S, 5.34. Found: C, 50.05; H, 3.97; N, 4.57; S, 5.42.

General procedure for deacetylation of nucleosides, synthesis of 6 and 7

TEA (1.0 mL) was added to a solution of protected nucleoside 4 or 5 (1.0 mmol) in methanol (10 mL) containing 3 drops of water and the mixture was stirred overnight at room temperature. The reaction was monitored by TLC (2% methanol and 98% CH2Cl2) and stirring was continued until completion. The solvent was removed under reduced pressure, the residue was treated with methanol and the resultant solution was concentrated until TEA was removed. The crude product 6 or 7 was purified by silica gel chromatography eluting with chloroform/methanol (9:1) and crystallized from methanol.

3-Cyano-1-(β-D-ribofuranosyl)-4-trifluoromethyl-6-(thiophen-2′-yl)-2-pyridone (6)

Pale yellow powder; yield 73%; mp 197°C; IR: 1655 (CO), 2206 (CN), 3428 cm−1 (-OH); 1H-NMR (DMSO-d6): δ 3.81–3.86 (m, 5 H, H-2″, H-3″, H-4″ and 2 H-5″), 4.81–4.84 (3 OH, exchangeable with D2O), 5.89 (d, 1H, H-1″, J=4.0 Hz), 6.34 (s, 1H, pyridine H-5), 6.80 (m, 1H, thiophene-H4), 7.18–7.19 (d, 1H, thiophene-H5, J=5.0 Hz), 7.73 (d, 1H, thiophene-H3, J=3.7 Hz); 13C-NMR (DMSO-d6): δ 75.3 (C5″), 75.6 (C3″), 75.9 (C2″), 82.5 (C-4″), 83.5 (C1″), 93.4 (pyridine-C5), 114.5 (pyridine-C3), 117.8 (CN), 120.5 (CF3), 123.4 (thiophene-C3), 124.9 (thiophene-C4), 126.3 (thiophene-C5), 137.9 (thiophene-C2), 141.5 (pyridine-C6), 152.2 (pyridine-C2), 166.8 (pyridine-C4). Anal. Calcd for C16H13F3N2O5S: C, 47.76; H, 3.26; N, 6.96; S, 7.97. Found: C, 47.81; H, 3.37; N, 6.87; S, 8.01.

3-Cyano-2-(β-D-glucopyranosyloxy)-4-trifluoromethyl-6-(thiophen-2′-yl)pyridine (7)

Pale yellow powder; yield 74%; mp 134°C; IR: 2206 (CN), 3392 cm−1 (sugar-OH); 1H NMR (DMSO-d6): δ 3.14–3.19 (m, 6H, H-2″, H-3″, H-4″, H-5″, H-6″a, H-6″b), 4.63–4.93 (4 OH, exchangeable with D2O), 6.97 (d, 1H, H-1″, J=8.0 Hz), 7.11 (m, 1H, thiophene-H4), 7.24 (s, 1H, pyridine-H5), 7.40 (d, 1H, thiophene-H5, J=5.0 Hz), 7.60 (d, 1H, thiophene-H3, J=3.7 Hz); 13C NMR (DMSO-d6): δ 62.8 (C5″), 64.0 (C3″), 70.4 (C2″), 72.4 (C4″), 97.3 (C1″), 112.1 (pyridine-C5), 113.2 (pyridine-C3), 122.0 (CN), 124.8 (CF3), 131.4 (thiophene-C3), 131.6 (thiophene-C4),134.6 (thiophene-C5), 143.9 (pyridine-C4), 146.9 (thiophene-C2), 157.2 (pyridine-C6), 164.8 (pyridine-C2). Anal. Calcd for C17H15F3N2O6S: C, 47.22; H, 3.50; N, 6.48; S, 7.42. Found: C, 47.27; H, 3.61; N, 6.39; S, 7.50.

General procedure for synthesis of 8a,b

To a solution of 2-pyridone 3 (5.0 mmol) in a mixture of acetonitrile (30 mL) and pyridine (2 mL), a solution of an aroyl chloride (10 mmol) in acetonitrile (5.0 mL) was added gradually with stirring at room temperature. The mixture was stirred at room temperature until the reaction was completed as indicated by TLC analysis. The mixture was concentrated under reduced pressure and the residue was washed with water (2×20 mL) and crystallized from ethanol to give the desired products 8a,b.

3-Cyano-6-(thiophen-2′-yl)-4-(trifluoromethyl)pyridin-2-yl 4′′-fluorobenzoate (8a)

Pale yellow crystals; yield 87%; mp 156°C; IR: 3089 (C-H, aromatic), 2235 (CN), 1754 (C=O), 1603 (C=C), 1451 cm−1 (C=N); 1H NMR (CDCl3): δ 7.29 (m, 1H, thiophene-H4), 7.64 (d, 2H, p-fluorobenzoyl, J=8.0 Hz ), 7.96–7.97 (d, 1H, thiophene-H5, J=5.0 Hz), 8.33 (d, 2H, p-fluorobenzoyl, J=8.0 Hz ), 8.36 (d, 1H, thiophene-H3, J=3.7 Hz ), 8.56 (s, 1H, pyridine-H5); 13C NMR (CDCl3): δ 95.8 (pyridine-C3), 112.1 (pyridine-C5), 113.8 (CN), 115.4 (CF3), 121.8 (aromatic carbons), 125.6 (thiophene-C3), 130.2 (thiophene-C4), 132.5 (thiophene-C5), 133.5, 134.8, 140.8 (aromatic carbons), 143.0 (pyridine-C4), 153.8 (thiophene-C2), 156.9 (pyridine-C6), 159.7 (C=O), 162.5 (C-F), 166.6 (pyridine-C2). Anal. Calcd for C18H10F4N2O2S: C, 54.82; H, 2.56; N, 7.10; S, 8.13. Found: C, 54.87; H, 2.67; N, 7.01; S, 8.21.

3-Cyano-6-(thiophen-2′-yl)-4-(trifluoromethyl)pyridin-2-yl 4′′-(trifluoromethyl) benzoate (8b)

Pale yellow crystals; yield 85%; mp 171°C; IR: 3085 (C-H, aromatic), 2231 (CN), 1760 (C=O), 1603 (C=C), 1421 cm−1 (C=N); 1H NMR (CDCl3): δ 7.29 (m, 1H, thiophene-H4), 7.48–7.52 (m, 2H, p-trifluoromethylbenzoyl), 7.95 (d, 1H, thiophene-H5, J=5.0 Hz), 8.26–8.29 (m, 2H, p-trifluoromethylbenzoyl), 8.35 (d, 1H, thiophene-H3, J=3.7 Hz ), 8.55 (s, 1H, pyridine-H5); 13C NMR (CDCl3): δ 95.8 (pyridine C3), 112.1 (pyridine-C5), 113.8 (CN), 116.1 (CF3), 120.4 (CF3), 123.2, 127.7 (thiophene-C3), 129.7 (thiophene-C4), 131.1 (thiophene-C5), 132.6, 133.3, 134.6 (aromatic carbons), 140.8 (pyridine-C4), 156.8 (thiophene-C2), 159.8 (pyridine-C6), 162.6 (C=O), 166.8 (pyridine-C2). Anal. Calcd for C19H10F6N2O2S: C, 51.36; H, 2.27; N, 6.30; S, 7.22. Found: C, 51.41; H, 2.38; N, 6.21; S, 7.30.

Antibacterial evaluations

Well diffusion assay

Two Gram positive bacteria (Bacillus infantis and Staphyloccus aureus) and two Gram negative bacteria (Escherichia coli and Stenotrophomonas maltophilia) were used. A Mueller Hinton agar (38.0 g of Mueller Hinton agar in 1000 mL of distilled water) was prepared, autoclaved and poured into the Petri dishes. It solidified at room temperature. The bacterial strains (106 cells/mL) were introduced onto the plates using a pipette and hockey sticks to spread them on the agar. All compounds were poured individually into the wells (50 μL/well). The wells were then incubated at 37°C for 24–48 h. The bacterial inhibition was determined by measuring the diameter of the inhibition zone (mm) using a transparent scale. Antibiotic amoxicillin (5 mg/mL) was used as a positive control at 50 μL/well.

Minimum inhibitory concentration (MIC)

This is the lowest concentration of the antimicrobial compound that inhibits the bacterial strain. Compounds were serially diluted with sterile distilled water and examined from lower dilution to higher dilution to find the MIC. Serially diluted compounds (100 μL) were added to a sterile nutrient broth (900 μL) and the bacterial cultures were inoculated as 105 cells/mL. Compounds and bacterial cultures in the nutrient broth were incubated at 37°C for 18–24 h. Controls included a nutrient broth with the compound only and another nutrient broth with the bacterial culture only. After incubation, the tubes were examined for turbidity, compared with controls and to confirm the results, loops of culture were inoculated in agar plates by streaking. The MIC was measured as the lowest concentration (mg/mL) of the extract resulting in no growth of the bacteria.

Acknowledgments

The authors wish to thank the Deanship of Graduate Studies and the Department of Chemistry, UAE University for financial support (Research Grant # 31S030).

References

[1] Saiki, A. Y.; Shen, L. L.; Chen, C. M.; Baranowski, J.; Lerner, C. G. DNA cleavage activities of Staphylococcus aureus gyrase and topoisomerase IV stimulated by quinolones and 2-pyridones. Antimicrob. Agents Chemother. 1999, 43, 1574–1577.10.1128/AAC.43.7.1574Search in Google Scholar PubMed PubMed Central

[2] Cocco, M. T. C.; Onnis, V. New bis(pyridyl)methane derivatives from 4-hydroxy-2-pyridones: synthesis and antitumoral activity. Eur. J. Med. Chem. 2003, 38, 37–47.10.1016/S0223-5234(02)00002-8Search in Google Scholar PubMed

[3] Abadi, A.; Al-Deeb, O.; Al-Afify, A.; El-Kashef, H. H. Synthesis of 4-alkyl (aryl)-6-aryl-3-cyano-2(1H)-pyridinones and their 2-imino isosteres as nonsteroidal cardiotonic agents. Farmaco1999, 54, 195–201.10.1016/S0014-827X(99)00004-XSearch in Google Scholar PubMed

[4] Oztürk, G.; Erol, D. D.; Uzbay, T.; Aytemir, M. D. Synthesis of 4(1H)-pyridinone derivatives and investigation of analgesic and antiinflammatory activities. Farmaco2001, 56, 251–256.10.1016/S0014-827X(01)01083-7Search in Google Scholar

[5] Storck, P. A.; Grierson, D. S. Tosylation/mesylation of 4-hydroxy-3-nitro-2-pyridinones as an activation step in the construction of dihydropyrido[3,4-b]benzo[f][1,4]thiazepin-1-one based anti-HIV agents. Tetrahedron Lett. 2005, 46, 2919–2922.10.1016/j.tetlet.2005.02.128Search in Google Scholar

[6] Li, Q. M. L.; Shen, L. L. The 2-pyridone antibacterial agents: bacterial topoisomerase inhibitors. Med. Res. Rev. 2000, 20, 231–293.10.1002/1098-1128(200007)20:4<231::AID-MED1>3.0.CO;2-NSearch in Google Scholar

[7] Pursor, S. M. P.; Swallow, S.; Gouverneur, V. Fluorine in medicinal chemistry. Chem. Soc. Rev.2008, 37, 320–330.10.1039/B610213CSearch in Google Scholar

[8] Isono, K. Nucleoside antibiotics: structure, biological activity, and biosynthesis. J. Antibiot. (Tokyo) 1988, 41, 1711–1739.10.7164/antibiotics.41.1711Search in Google Scholar

[9] Kimuraa, K-I.; Buggb, T. D. H. Recent advances in antimicrobial nucleoside antibiotics targeting cell wall biosynthesis. Nat. Prod. Rep.2003, 20, 252–273.10.1039/b202149hSearch in Google Scholar

[10] Bzowska, A.; Kulikowska, E.; Shugar, D. Purine nucleoside phosphorylases: properties, functions, and clinical aspects. Pharmacol. Ther.2000, 88, 349–425.10.1016/S0163-7258(00)00097-8Search in Google Scholar

[11] Mills, S. D.; Eakin, A. E.; Buurman, E. T.; Newman, J. V.; Gao, N.; Huynh, H.; Johnson, K. D.; Lahiri, S.; Shapiro, A. B.; Walkup, G. K.; et al. Novel bacterial NAD+-dependent DNA ligase inhibitors with broad-spectrum activity and antibacterial efficacy in vivo. Antimicrob Agents Chemother. 2010, 55, 1088–1096.10.1128/AAC.01181-10Search in Google Scholar PubMed PubMed Central

[12] Ahn, Y. J.; Park, S. J.; Lee, S. G.; Shin, S. C.; Choi, D. H. Cordycepin: selective growth inhibitor derived from liquid culture of Cordyceps militaris against Clostridium spp. J. Agric. Food Chem.2000, 48, 2744–2748.10.1021/jf990862nSearch in Google Scholar PubMed

[13] Shimada, N.; Hasegawa, S.; Harada, T.; Tomisawa, T.; Fujii, A.; Takita, T. Oxetanocin, a novel nucleoside from bacteria. J. Antibiot. (Tokyo)1986, 39, 1623–1625.10.7164/antibiotics.39.1623Search in Google Scholar PubMed

[14] Lee, R. T.; Lee, Y. C. Synthesis of 3-(2-aminoethylthio)propyl glycosides. Carbohyd. Res.1974, 37, 193–201.10.1016/S0008-6215(00)87074-3Search in Google Scholar

[15] Kazimierczuk, Z.; Cottam, H. B.; Revankar, G. R.; Robins, R.; K. Synthesis of 2-deoxynucleotides via a novel direct stereospecific sodium salt glycosylation procedure. J. Am. Chem. Soc.1984, 106, 6379–6382.10.1021/ja00333a046Search in Google Scholar

[16] Andrzejewska, M.; Kamiński, J.; Kazimierczuk, Z. Microwave induced synthesis of ribonucleosides on solid support. Nucleosides, Nucleotides, Nucleic Acids2002, 21, 73–78.10.1081/NCN-120006532Search in Google Scholar PubMed

[17] Vorbrüggen, H.; Bennua, B. New simple nucleoside synthesis. Tetrahedron Lett.1978, 19, 1339–134210.1016/0040-4039(78)80123-3Search in Google Scholar

[18] Niedballa, U.; Vorbrueggen, H. Synthesis of nucleosides 17. A general synthesis of N-glycosides. 6. On the mechanism of the stannic chloride catalyzed silyl Hilbert-Johnson reaction. J. Org. Chem.1976, 41, 2084–2086.10.1021/jo00874a002Search in Google Scholar PubMed

[19] Davoodnia, A.; Attar, P.; Morsali, A.; Eshghi, H.; Hoseini, N. T.; Khadem, S. Experimental and theoretical studies on the tautomerism in 2-aminopyridines and 2(1h)-pyridinones: synthesis of 2-amino-4-aryl-3-cyano-6-(3,4-dimethoxyphenyl)pyridines and 4-aryl-3-cyano-6-(3,4-dimethoxyphenyl)-2(1H)-pyridinones. Bull. Korean Chem. Soc. 2011, 32, 1873–1878.10.5012/bkcs.2011.32.6.1873Search in Google Scholar

[20] Alneyadi, S. S.; Shehadi, I. A.; Abdou, I. M. Synthesis and anti-proliferative activity of pyridine O-galactosides and 4-fluorobenzoyl analogues. Heterocycl. Commun.2015, 21, 285–290.10.1515/hc-2015-0125Search in Google Scholar

Received: 2017-2-1
Accepted: 2017-2-2
Published Online: 2017-4-19
Published in Print: 2017-6-27

©2017 Walter de Gruyter GmbH, Berlin/Boston

This article is distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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  2. Editorial
  3. Carbohydrate chemistry/glycoscience
  4. Reviews
  5. Boron-based small molecules in disease detection and treatment (2013–2016)
  6. Impact of modified ribose sugars on nucleic acid conformation and function
  7. Preliminary Communication
  8. Crystallization-induced amide bond formation creates a boron-centered spirocyclic system
  9. Research Articles
  10. Anion and sugar recognition by 2,6-pyridinedicarboxamide bis-boronic acid derivatives
  11. Synthesis of biotinylated bivalent zanamivir analogs as probes for influenza viruses
  12. Synthesis of silodosin glucuronide and its deuterated counterpart: solving a problematic O-glycosylation of a nitrogen-containing molecule
  13. Synthesis and antimicrobial activity of 4-trifluoromethylpyridine nucleosides
  14. Synthesis of anti-inflammatory 2,3-unsaturated O-glycosides using conventional and microwave heating techniques
  15. Synthesis of various β-D-glucopyranosyl and β-D-xylopyranosyl hydroxybenzoates and evaluation of their antioxidant activities
  16. Synthesis of carbohydrate-substituted isoxazoles and evaluation of their antitubercular activity
  17. Synthesis and bioactivity of novel C2-glycosyl triazole derivatives as acetylcholinesterase inhibitors
  18. Modification of bovine serum albumin with aminophenylboronic acid as glycan sensor based on surface plasmon resonance and isothermal titration calorimetry
https://doi.org/10.1515/hc-2017-0019
Keywords for this article
antimicrobial; fluoropyridine; gHMBC; nucleosides; synthesis
Creative Commons
BY-NC-ND 3.0

Articles in the same Issue

  1. Frontmatter
  2. Editorial
  3. Carbohydrate chemistry/glycoscience
  4. Reviews
  5. Boron-based small molecules in disease detection and treatment (2013–2016)
  6. Impact of modified ribose sugars on nucleic acid conformation and function
  7. Preliminary Communication
  8. Crystallization-induced amide bond formation creates a boron-centered spirocyclic system
  9. Research Articles
  10. Anion and sugar recognition by 2,6-pyridinedicarboxamide bis-boronic acid derivatives
  11. Synthesis of biotinylated bivalent zanamivir analogs as probes for influenza viruses
  12. Synthesis of silodosin glucuronide and its deuterated counterpart: solving a problematic O-glycosylation of a nitrogen-containing molecule
  13. Synthesis and antimicrobial activity of 4-trifluoromethylpyridine nucleosides
  14. Synthesis of anti-inflammatory 2,3-unsaturated O-glycosides using conventional and microwave heating techniques
  15. Synthesis of various β-D-glucopyranosyl and β-D-xylopyranosyl hydroxybenzoates and evaluation of their antioxidant activities
  16. Synthesis of carbohydrate-substituted isoxazoles and evaluation of their antitubercular activity
  17. Synthesis and bioactivity of novel C2-glycosyl triazole derivatives as acetylcholinesterase inhibitors
  18. Modification of bovine serum albumin with aminophenylboronic acid as glycan sensor based on surface plasmon resonance and isothermal titration calorimetry
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