# Thio Analogs of Pyrimidine Bases: Synthesis, Spectroscopic Study, andIn Silico Biological Activity Evaluation of New 2-o-(m- and p-)Chlorobenzylthio-6-Methyl-5-Piperidino-(Morpholino-)Methyluracils

Authors: Tomasz Pospieszny; Marcin Szymankiewicz; Elżbieta Wyrzykiewicz
Journal: ISRN Organic Chemistry
 (2011)

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## Abstract

Six new 2-o-(m- and p-)chlorobenzylthio-6-methyl-5-piperidino-(or morpholino-) methyluracils have been prepared. The structures of these compounds were confirmed by spectroscopic (FT-IR, UV-Vis, 1H NMR, 13C NMR, and HMBC) and elemental analyses. Estimation of pharmacotherapeutic potential has been made for synthesized compounds on the basis of prediction of activity spectra for substances (PASS).


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## Body

## 1. Introduction

Thio derivatives of pyrimidine bases have remarkably contributed to biological and medicinal chemistry. Chemical modification of these compounds have led to a large number of mono- and di-S and N-substituted analogs showing therapeutic properties, especially antivirial, antithyroid, and antitumor activities [1–7]. The antimetabolites of 5,6-dimethyluracil 5-morpholinomethyl-6-methyl-2-thiouracil [8] and 5-piperidinomethyl-6-methyl-2-thiouracil [9] have been synthesized via the Mannich reaction. However, to the best of our knowledge no work has been published on the synthesis as well as on physicochemical properties of the monochlorobenzylthio-substituted derivatives of these compounds. This fact has stimulated us to investigate the reaction of chlorobenzylation of 2-thio-5-piperidinomethyl-6-methylthiouracil and 2-thio-5-morpholinomethyl-6-methylthiouracil as well as the Mannich reaction of 2-o-(m- and p-)chlorobenzylthio-6-methylthiouracils, formaldehyde, and piperidine (or morpholine). Recently novel pharmacological action of 2,4-di-o-(m- and p-)bromo-(chloro- and nitro-)benzylthio-5-bromouracils (and 6-methyluracils) [10] as well as disulfides of N,O-(N,N- or O,O-)-di- and N,N,O-tri-(o-, m- and p-)-bromobenzyl-2-thiouracils [11] has been found on the basis of the computer-aided drug discovery approach with the compounds program Prediction of Activity Spectra for Substances (PASS) [12–15]. Since only the structural formula of the chemical compound is necessary to obtain a PASS prediction, this approach was used in the present work. This paper deals with the synthesis and physicochemical properties of 1–6. Additionally, the analysis of biological activity spectra prediction for 1–6 made in this paper is a good example of in silico studies of chemical compounds.


## 2. Results and Discussion

A series of six new 2-o-(m- and p-)chlorobenzylthio-5-piperidinomethyl-6-methyluracils 1–3 and 2-o-(m- and p-)chlorobenzylthio-5-morpholinomethyl-6-methyluracils 4–6were synthesized by the reaction of 2-thio-5-piperidinomethyl-6-methyluracil or 2-thio-5-morpholinomethyl-6-methyluracil in 3 N NaOH in methanol with o-(m- and p-)chlorobenzyl chlorides at room temperature for 24 h (Scheme 1). Compounds 1, 3, 4, and 6 were also produced in well-known Mannich reaction [16] from 2-o-(and p-)chlorobenzylthio-6-methyluracils [17] when refluxed with paraformaldehyde and piperidine (or morpholine) in ethanol (Scheme 2). Compounds 2 and 5 were not produced in the Mannich reaction of relatively soft 2-m-chlorobenzylthio-6-methyluracils with paraformaldehyde and piperidine (or morpholine) when heated in ethanol (Scheme 2). The 2 o-(m- and p-)chlorobenzylthio-containing compounds 1–6 were confirmed by examination of their UV/Vis, FT-IR, 1H NMR and 13C NMR spectra (Tables 1 and 2), and HMBC (Table 3) as well as elemental analyses (Table 4).Table 1
FT-IR, UV-Vis, and1H NMR data of compounds 1–6.
Comp.UV/Vis (CH3OH) λmax nm (log ε)FT-IR cm−1(KBr)1H NMR (DMSOd6) ppmS–CH2(ν)C–Cl (ν)S–CH2 (s)C5–CH2 (s)C6–CH3 (s)S–CH2(δ)C–Cl (δ)1250.0 (3.03)2857.51052.54.393.582.231447.4820.32250.0 (3.00)2856.81035.04.303.582.221446.3822.13249.5 (2.87)2864.61055.34.293.572.221450.9819.64247.0 (3.27)2852.51053.14.463.292.331444.0814.15245.5 (3.34)2858.51059.64.363.292.311456.3813.06247.5 (3.23)2858.81091.34.353.282.311444.7809.6Table 2
13C NMR data of compounds 1–6.
CarbonCompound123456C-2167.69167.70168.05163.98163.68163.83C-4161.82162.81163.19163.11162.73162.89C-5110.04110.01110.02114.11113.98114.71C-6162.03161.88162.11159.09158.81159.06C-720.9220.9020.9221.2921.2221.30C-853.2453.7153.1553.0553.0453.09C-931.5832.8132.6931.5532.7332.60X23.0723.0423.01———C-1024.6324.5724.5266.2266.1466.21C-1152.6752.6652.7551.6551.5951.62C-1′135.56141.18137.82134.93140.29136.93C-2′133.09128.77130.85133.37128.88131.01C-3′129.15132.52128.12129.41132.50128.33C-4′128.87126.67131.45129.41126.94131.77C-5′127.05129.96128.12127.32130.04128.33C-6′131.31127.55130.85131.66127.67131.01Table 3
The HMBC correlations between protons and carbons of compounds1–6.
CompoundCarbon atomδC (ppm)HMBC1H/13C1C-2167.69S–CH2C-4161.82C5–CH2C-6162.03C6-CH32C-2167.70S–CH2C-4162.81C5–CH2C-6161.88C6-CH33C-2168.05S–CH2C-4163.19C5–CH2C-6162.11C6–CH34C-2163.98S–CH2C-4163.11C5–CH2C-6159.09C6–CH35C-2163.68S–CH2C-4162.73C5–CH2C-6158.81C6–CH36C-2163.83S–CH2C-4162.89C5–CH2C-6159.06C6–CH3Table 4
Physical and analytical data of compounds1–6.
Comp.Formula MWYield [%]M.p. [°C]Rf TLC*AnalysisCalculatedFoundCHNCHN1C18H22N3SOCl 363.9058183-30.2159.125.8911.5559.005.6011.402C18H22N3SOCl 363.9035147-80.2059.125.8911.5559.595.7211.603C18H22N3SOCl 363.906799-1000.2359.125.8911.5559.105.8011.284C17H20N3SO2Cl 365.8862175-60.3055.815.5111.4855.535.2411.215C17H20N3SO2Cl 365.8823134-50.3155.815.5111.4855.825.3411.166C17H20N3SO2Cl 365.8856177-80.3255.815.5111.4855.585.3011.24*CHCl3 : CH3OH, 10 : 1.Scheme 1Scheme 2The1H NMR and 13C NMR data of 1–6 are given in Tables 1 and 2, respectively. Assignments of the 1H NMR and 13C NMR resonances of these compounds were deduced on the basis of the signal multiplicities and by the corrected application of two-dimensional NMR technique 1H-1H COSY and HMBC. The 1H NMR spectra of 1–6 reveal singlets of S–CH2 at 4.29–4.46 ppm. The singlets of C5–CH2 of 1–6 are situated at 3.28–3.58 ppm, and the singlets of C6–CH3 of 1–6 are situated at 2.22–2.33 ppm, respectively.The13CNMR spectra of compounds 1–6 in DMSOd6 showed  characteristic signals in the range of 31.55–32.81 ppm and 53.04–53.71 ppm assigned to S–CH2 and N–CH2, respectively. The thiouracil ring exhibited signals in the range 110.01–114.71 ppm and 158.81–162.11 ppm assigned to C5=C6, respectively. The 13C NMR spectra of compounds 1–6 showed the presence of a methyl group from the 6-methyl-2-thiouracil ring at 20.90–21.30 ppm.The HMBC spectrum clearly shows the connectivities of all hydrogen and carbon atoms involved, including quaternary carbons. The HMBC results allow an unequivocal assignment ofS-substitution of benzyl group at uracil ring of 1–6(Table 3). The HMBC experiment is conducted without 13C decoupling so that correlations via one or more bond can be discerned and one-bond correlation affords double cross-peaks in the 1H dimension. For compounds 1–6 the 1H NMR spectrum exhibits three singlets at 4.29–4.46, 3.28–3.58, and 2.22–2.33 ppm ascribed to protons of S–CH2, C5–CH2 and C6–CH3, respectively. The HMBC of 1–6 shows peaks corresponding to two-bond correlations for C6–CH3/C6 (158.81–162.11 ppm) and three-bond correlations for S–CH2/C2(163.68–168.05 ppm) and C5–CH2/C4 (161.82–163.19 ppm).The FT-IR spectra of1–6 show absorption bands of medium intensities in the region 809–820 cm−1 assigned to ν C–Cl vibration as well as in the region 1035–1091 cm−1 assigned to δ C–Cl vibration (Table 1). The FT-IR spectra of 1–6 show also absorption bands in the region 2852–2864 cm−1 assigned to ν CH2–S as well as in the region 1444–1447 cm−1 assigned to δ CH2–S vibration (Table 1). The UV/Vis spectra of 1–6 show λmax in the range 245–250 nm (Table 1).In the present paper the biological activity spectra were predicted for all six synthesized compounds (1–6) using PASS [12–15]. We have also selected the types of activities that were predicted for a potential compound with the highest probability (focal activities). They are presented in Table 5. According to these data the most frequently predicted types of biological activities are antiviral (Influenza), antiseborrheic, and prolyl aminopeptidase inhibitor. It ought to be pointed out that in the series of compounds 1, 3 and 6 such activity as mucomembranous protector has also been predicted, as well as in the series of compounds 2, 3, 5, and 6 such activity as prolyl aminopeptidase inhibitor.Table 5
PA values for predicted biological activity of compounds1–6.
CompoundFocal predicted activity (PA > 0.7)1Mucomembranous protector (0.777)Antiviral (Influenza) (0.711)2Cardiotonic (0.790)Antiviral (Influenza) (0.704)Antiseborrheic (0.768)Prolyl aminopeptidase inhibitor (0.751)3Mucomembranous protector (0.796)Antiviral (Influenza) (0.711)Antiseborrheic (0.780)Prolyl aminopeptidase inhibitor (0.720)4Antiviral (Influenza) (0.721)5Antiviral (Influenza) (0.711)Antiseborrheic (0.768)Prolyl aminopeptidase inhibitor (0.735)6Mucomembranous protector (0.712)Antiviral (Influenza) (0.722)Antiseborrheic (0.778)Prolyl aminopeptidase inhibitor (0.735)


## 3. Conclusions

The reaction of 2-thio-5-piperidinomethyl-6-methyluracil and 2-thio-5-morpholinomethyl-6-methyluracil witho-(m- and p-)chlorobenzyl chlorides in 3 N NaOH in methanol at room temperature leads to 2-o-(m- and p-)chlorobenzylthio-5-piperidinomethyl-6-methyluracils 1–3 and 2-o-(m- and p-)-chlorobenzylthio-5-morpholinomethyl-6-methyluracils 4–6. The Mannich reaction of 2-o-(and p-)chlorobenzylthio-6-methyluracils with paraformaldehyde and piperidine (or morpholine) refluxed in ethanol leads to 1, 3, 4, and 6. The results obtained by PASS method of identification of the prospective pharmacological properties of 1–6 exhibit the possibility of finding new pharmacological agents from this class of compounds.


## 4. Experiment

The purity of all described compounds was checked by melting points, TLC, and elemental analyses. Melting points (uncorrected) were determined on a Boetius microscope hot stage. Rf values refer to silica gel F254 TLC plates (Merck) developed with CHCl3 : CH3OH (10 : 1) and observed under UV light (λ=254 and 366 nm). UV/Vis spectra were recorded with a SPECORD UV/Vis Spectrophotometer in methanol. IR spectra were recorded with FT-IR Bruker IFS-113 Spectrophotometer in KBr pellets. The 1H NMR (300 MHz) and 13C NMR (75 MHz) spectra were determined with Varian Gemini 300 spectrometer in DMSOd6 solution at a concentration between 0.25 and 0.40 M in the 5 mm sample tubes at ambient temperature. Chemical shifts are given in δ scale (ppm). Elemental analyses were performed with a Vector Euro EA 3000 analyzer.2-thio-5-piperidinomethyl-6-methyluracil [9], 2-thio-5-morpholinomethyl-6-methyl-uracil [8], and 2-o-(m- and p-)-chlorobenzylthio-6-methyluracils [17] have been obtained according to the literature.The synthesis of 2-o-(and p-)chlorobenzylthio-5-piperidinomethyl-6-methyluracils (1 and 3) and 2-o-(and  p-)chlorobenzylthio-5-morpholinomethyl-6-methyluracils (4and6) is as follows.General procedure A: 0.2 g (0.8 mmole) of 2-thio-5-piperidino-(morpholino-)-methyl-6-methyluracils [8, 9] was dissolved with stirring in room temperature in 2.5 mL of 3 N NaOH in methanol. Next, to the solution 0.116 mL (0.9 mmole) of o-chlorobenzyl chloride or 0.146 g (0.9 mmole) of p-chlorobenzyl chloride was added. After stirring at room temperature for 24 hours, the obtained crude product was filtered off and crystallized from methanol.The synthesis of 2-m-chlorobenzylthio-5-piperidinomethyl-6-methyluracils (2) and 2-m-chlorobenzylthio-5-morpholinomethyl-6-methyluracils (5) is as follows.General procedure A: 0.2 g (0.8 mmole) of 2-thio-5-piperidino-(morpholino-)methyl-6-methyluracils [8, 9] was dissolved with stirring in room temperature in 2.5 mL of 3 N NaOH in methanol. Next, to the solution 0.116 mL (0.9 mmole) of m-chlorobenzyl chloride was added. The reaction mixture was stirred in room temperature for 24 hours and after that time 5 mL distilled water was added. The obtained crude product was collected by filtration, washed with distilled water, and dried in the exicator. The obtained dry solid was dissolved in 10 mL of CHCl3 and separated by silica gel column chromatography (Merck 203–400 mesh) using the following solvent mixtures: CHCl3 : CH3OH 50 : 1 (40 mL), 40 : 1 (40 mL), 30 : 1 (30 mL), 20 : 1 (30 mL), and 10 : 1 (20 mL). The fractions of 20 mL were collected. On the basis of analytical TLC fractions of product desired were obtained by combining 20 mL fractions. They were concentrated on a rotary evaporator. Compounds 2 and 5 were shown to by analytically pure.The synthesis of 2-o-(and p-)chlorobenzylthio-5-piperidinomethyl-6-methyluracils (1 and 3) and 2-o-(and  p-)chlorobenzylthio-5-morpholinomethyl-6-methyluracils (4and6) is as follows.General procedure B: A mixture of 0.1 g (0.38 mmole) 2-o-(or p-)chlorobenzylthio-6-methyluracils, 0.024 g (0.4 mmole) paraformaldehyde, and 0.0035 mL (0.4 mmole) morpholine (or 0.0046 mL, 0.4 mmole piperidine) was suspended in 6 mL of ethanol (99.8%) and refluxed for 8 hours. The precipitated solid was isolated by filtration, dried in room temperature, and recrystallized from methanol.



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