- Research article
- Open Access
Three-component synthesis of pyrano[2,3-d]-pyrimidine dione derivatives facilitated by sulfonic acid nanoporous silica (SBA-Pr-SO3H) and their docking and urease inhibitory activity
- Ghodsi Mohammadi Ziarani†1Email author,
- Sakineh Faramarzi1,
- Shima Asadi1,
- Alireza Badiei2,
- Roya Bazl3 and
- Massoud Amanlou†3Email author
© Mohammadi Ziarani et al.; licensee BioMed Central Ltd. 2013
- Received: 12 September 2012
- Accepted: 30 December 2012
- Published: 5 January 2013
A straightforward and efficient method for the synthesis of pyrano[2,3-d]pyrimidine diones derivatives from the reaction of barbituric acid, malononitrile and various aromatic aldehydes using SBA-Pr-SO3H as a nanocatalyst is reported.
Reactions proceed with high efficiency under solvent free conditions. Urease inhibitory activity of pyrano[2,3-d]pyrimidine diones derivatives were tested against Jack bean urease using phenol red method. Three compounds of 4a, 4d and 4l were not active in urease inhibition test, but compound 4a displayed slight urease activation properties. Compounds 4b, 4k, 4f, 4e, 4j, 4g and 4c with hydrophobic substitutes on phenyl ring, showed good inhibitory activity (19.45-279.14 μM).
The compounds with electron donating group and higher hydrophobic interaction with active site of enzyme prevents hydrolysis of substrate. Electron withdrawing groups such as nitro at different position and meta-methoxy reduced urease inhibitory activity. Substitution of both hydrogen of barbituric acid with methyl group will convert inhibitor to activator.
- Barbituric acid
- Pyrano[2,3-d]pyrimidine diones
- Multicomponent reaction (MCRs)
- Urease inhibitory
Pyran derivatives are ordinary structural subunits in a variety of important natural products, including carbohydrates, alkaloids, polyether antibiotics, pheromones, and iridoids . Uracil and its fused derivatives, such as pyrano[2,3-d pyrimidines, pyrido[2,3-d pyrimidines or pyrimido[4,5-d pyrimidines are well recognized by synthesis as well as biological chemists.
These annelated uracils have received considerable attention over the past years due to their wide range of biological activity. Compounds with these ring systems have diverse pharmacological properties such as antiallergic , antihypertensive , cardiotonic , bronchiodilator , antibronchitic , or antitumour activity . The synthesis of the mentioned compounds containing a pyran and an uracil ring poses significant synthetic challenges. Therefore, for the preparation of these complex molecules large efforts have been directed towards the synthetic manipulation of uracils. As a result, a number of reports have described in literature [8–12] which usually require drastic conditions, long reaction times and complex synthetic pathways and the yields are poor. Thus new routes for the synthesis of these molecules have attracted considerable attention in search for a rapid entry to these heterocycles.
The general procedures for the preparation of pyrano[2,3-d pyrimidine-2,4(1H,3H)-diones include the reaction of arylidenemalononitriles with barbituric acid under traditional hot reaction conditions [13, 14] or microwave irradiation . In these methods the arylidenemalononitriles are previously derived from malononitrile and aldehydes. Recently, direct condensation of aldehydes, malononitrile and barbituric acid in aqueous media has been reported under ultrasound irradiation , or catalyzed by diammonium hydrogen phosphate .
Different catalysts such as L-proline , N-methylmorpholine , [BMIm]BF4, 1,4-dioxane [13, 21], H14[NaP5W30O110 and [K Al(SO4)2 under heating also 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP)  and L-proline  under room temperature condition have been researched for the synthesis of pyrano[2,3-d pyrimidine diones derivatives. In addition, Et3N was examined under microwave irradiation . The catalyst free procedures for the preparation of the pyrano pyrimidine diones were also investigated using microwave irradiation , ultrasonic , heating with water  and ball-milling technique .
Mesoporous materials are a special type of nanomaterials with ordered arrays of uniform nanochannels. These materials have important applications in a wide variety of fields such as separation, catalysis, adsorption, advanced nanomaterials, etc [28–33]. SBA-15 has many advantages such as: largest pore-size mesoporous material with highly ordered hexagonally arranged meso-channels, with thick walls, adjustable pore size from 3 to 30 nm, and high hydrothermal and thermal stability [34–38], therefore it is expected to be an useful catalyst in the synthesis of organic compounds.
The surface of SBA-15 was modified by acidic functional groups (e.g., -SO3H) to prepare nano-solid acid catalyst which can use in the synthesis of various heterocyclic compounds . Recently, we have also reported the use of this catalyst for the synthesis of quinoxaline derivatives , polyhydroquinolines , triazoloquinazolinones and benzimidazoquinazolinones .
Moreover, to the best of our knowledge there is no report on the use of these materials as nanoreactors in the synthesis of pyrano pyrimidine diones derivatives. In the present work, we report our results on the research of convenient and green way for the synthesis of pyrano[2,3-d]pyrimidine diones derivatives using SBA-Pr-SO3H as a nanocatalyst and their urease inhibitory activity was investigated.
Gc-Mass analysis was performed on a Gc-Mass model: 5973 network mass selective detector, Gc 6890 Agilent. IR spectra were recorded from KBr disk using a FT-IR Bruker Tensor 27 instrument. Melting points were measured by using the capillary tube method with an electro thermal 9200 apparatus. The 1H-NMR (250 MHZ) was run on a Bruker DPX, 250 MHZ. Nitrogen adsorption and desorption isotherms were measured at -196°C using a Japan Belsorb II system after the samples were vacuum dried at 150°C overnight. Surface areas were calculated by the Brunauer-Emmett-Teller (BET) method, and pore sizes were calculated by the Barrett-Joyner-Halenda (BJH) method. Thermogravimetry analysis (TGA) was carried out in Perkin Elmer Pyris Diamond instrument from ambient temperature to 800°C using 20°C/min ramp rate.
Preparation of catalyst
Synthesis and functionalization of SBA-15
The nanoporous compound SBA-15 was synthesized and functionalizaed according to our previous report and the modified SBA-15-Pr-SO3H was used as nanoporous solid acid catalyst in the following reactions [40–43].
General procedure for the preparation pyrano[2,3-d]pyrimidine diones
Spectral data for product
7-Amino-6-cyano-5-(3-methylphenyl)-5H-pyrano[2,3-d]pyrimidine-2,4(1H,3H)-diones 4f: IR (KBr): υmax= 3411 and 3320 (NH2), 2961 and 2740 (CN), 1733 and 1700 (C=O) cm-1. 1H NMR (250 MHz, CDCl3): δ = 2.47 (s, 3H, CH3), 4.13 (s, 1H, CH), 6.95-7.17 (m, 6H, ArH & NH2), 11.09 (s, 1H, NH) 12.00 (s, 1H, NH) ppm. Mass (m/z): 296 (M + ), 285, 149 (100).
7-Amino-6-cyano-5-(3-methoxylphenyl)-5H-pyrano[2,3-d]pyrimidine-2,4(1H,3H)-diones 4h: IR (KBr): υmax= 3183 and 2834 (NH2), 2246 and 2200 (CN), 1690 and 1538 (C=O), 1459, 1375 cm-1. 1H NMR (250 MHz, CDCl3): δ = 3.35 (s, 3H, OCH3), 4.16 (s, 1H, CH), 6.96-7.78 (m, 4H, ArH), 8.48 (s, 2H, NH2) 11.03 (s, 1H, NH), 11.77 (s, 1H, NH) ppm. Mass (m/z): 312 (M+), 276, 230, 215.
7-Amino-6-cyano-5-(2,6-dichlorophenyl)-5H-pyrano[2,3-d]pyrimidinone 4k: IR (KBr): υmax= 3368, 3337, 3148 and 3038 (NH2), 2930 and 2196 (CN), 1703 and 1664 (C=O), 1102, 1283, 763 cm-1. 1H NMR (250 MHz, CDCl3): δ = 5.28 (s, 1H, CH), 7.94 (s, 2H, NH2), 7.24- 7.36 (m, 5H, -ArH & NH2), 11.05 (s, 1H, NH), 12.20 (s, 1H, NH) ppm. Mass (m/z): 352 (M+), 316, 282, 267, 257, 191, 167, 122, 82.
7-Amino-6-cyano-1,3-dimethyl-5-(4-Hydroxyphenyl)-1,5-dihydro-pyrano[2,3-d]pyrimidine-2,4-dione 4l: IR (KBr): υmax= 3415, 3315, 3203 and 3020 (NH2), 2192 (CN), 1688, 1659 and 1529 (C=O), 1348 cm-1. 1H NMR (250 MHz, CDCl3): δ = 3.17 (s, 3H, CH3), 3.40 (s, 3H, CH3), 4.40 (s, 1H, CH), 6.83-8.25 (m, 6H, ArH, & NH2) ppm. Mass (m/z): 326 (M+), 327(M+1), 306, 281, 149 (100).
AutoDockTools 1.5.4 (ADT) , Autogrid 4.2  and Autodock 4.2  were used to prepare input files, calculate grid box and docking experiments. A grid map consisted of 40 × 40 × 40 Å points around the active site was used. The center of the grid was set to the average coordinates of the two Ni2+ ions in the α chain of H. pylori urease (pdb ID: 3LA4). A Lamarckian genetic algorithm (LGA) was used for the conformational search. The reliability of the applied docking protocol was assessed by re-docking acetohydroxamic acid (AHA) into the active site of the H. pylori urease. Each Lamarckian job consisted of 250 runs. The initial population was 150 structures, and the maximum number of energy evaluations and generations was 2.5 × 107. The other parameters were set to default values. The final structures were clustered and ranked according to the most favorable docking energy. This protocol was then similarly applied to all synthesized compounds .
The computational studies were carried out on a computer cluster comprising four sets of HP Prolient ML370-G5 tower servers equipped with two quad-core Intel Xeon E5355 processors (2.66 GHz) and 4 GB of RAM, running a Linux platform (SUSE 10.2).
Urease inhibitory assay
All the chemicals used were of analytical grade from Merck Co., Germany. All aqueous solutions were prepared in MilliQ (Millipore, USA) water. Jack-bean urease was obtained from Merck (5 units/mg). After proper dilution, the concentration of enzyme solution adjusts at 2 mg/ml which is determined by UV spectroscopy at λ = 280 nm. Urease activity was measured by rapid phenol red urease test contains phenol red 0.1% (w/v) and 100 mM urea in 10 mM phosphate buffer, pH 7.0. Based on this method, the colour change from yellow (pH 6.8) to bright pink (pH 8.2) of phenol red pH indicator as a result of urea hydrolysis to ammonia was measured. The urease activity of the synthesized compounds (10 μl in DMSO) was monitored spectrophotometrically at 560 nm after incubation at 37°C for 30 min .
In this article, we want to report the use of SBA-Pr-SO3H as a nano and green solid acid catalyst and nano- reactor in the synthesis of 7-amino-6-cyano-5-aryl-5H-pyrano[2,3-d]pyrimidinones by the Knoevenagel–Michael condensation reaction. The procedure consisted of the mixture of malonitrile, aromatic aldehydes, and barbituric acid derivatives. The reaction proceeded in high yields in the presence of SBA-Pr-SO3H as catalyst at room temperature and solvent free conditions to obtain our desired products 4a-4l (Scheme 1).
Optimization of the reaction conditions in the synthesis of 4i
Synthesis of pyrano[2,3- d ]pyrimidine diones derivatives 4 under optimized conditions
Comparison of SBA-Pr-SO 3 H and various catalysts in the synthesis of pyrano[2,3- d ]pyrimidine diones derivatives 4
30 min–12 h
Preparation of catalyst
The pyrano[2,3-d pyrimidine diones structurally similar to barbituric acids. The antibacterial and urease inhibitory activity of barbituric acid derivatives were reported [46, 48, 49]. Many urease inhibitors have been synthesized and tested, but because of their toxicity and instability use of them in vivo is impossible [48–50]. Thus, the search is still on for finding strong and specific urease inhibitors.
Urease inhibitory activities (IC 50 in μM) and interaction energies (kcal mol −1 ) of pyrano[2,3- d ]pyrimidine diones derivatives 4
Docking energy (kcal/mol)
We gratefully acknowledge for financial support from the Research Council of Alzahra University and University of Tehran and Tehran University of Medical Sciences.
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