|Year : 2016 | Volume
| Issue : 3 | Page : 181-187
Synthesis, characterization and in silico biological activity of some 2-(N,N-dimethyl guanidinyl)-4,6-diaryl pyrimidines
Rajasekhar Komarla Kumarachari1, Sivakumar Peta2, Abdrrahman Shemsu Surur1, Yenus Tadesse Mekonnen1
1 Department of Pharmaceutical Chemistry, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, India
2 Department of Pharmaceutical Chemistry, Gokula Krishna College of Pharmacy, Sullurpeta, Andhra Pradesh, India
|Date of Submission||10-Jun-2015|
|Date of Decision||25-Jul-2015|
|Date of Acceptance||06-Oct-2015|
|Date of Web Publication||22-Jun-2016|
Rajasekhar Komarla Kumarachari
Department of Pharmaceutical Chemistry, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar
Source of Support: None, Conflict of Interest: None
| Abstract|| |
Introduction: As pyrimidine is a basic nucleus in DNA and RNA, it has been found to be associated with diverse biological activities.Pyrimidine derivatives were reported to possess anticonvulsant, antimicrobial, anti-inflammatory, antitumor, and antihistaminic. Recently, our team reported the anti-inflammatory and antimicrobial evaluation of some pyrimidines. Objective: To synthesize, predict and evaluate biological activity of some 2-(N,N-dimethyl guanidinyl)-4,6-diaryl pyrimidines. Experimental: seven new pyrimidines were synthesized by following the standard procedures using substituted aromatic aldehydes, methyl ketones and metformin. After the biological activity was predicted using PASS, Molinspiration and Osiris property explorer, their anthelmintic activity was evaluated using Pheretima posthuma. The structural assignment of the title compounds (P1-7) has been made on the basis of elemental analysis, infrared, 1H-nuclear magnetic resonance and Mass spectral studies. Results: All the synthesized compounds were found to obey Lipinski's rule. All the synthesized compounds scored good bioactivity values as GPCR ligands and kinase inhibitors. Among the test compounds, P5 was found to be more potent anthelmintic inducing paralysis in 36-48 minutes and death in 40-51 minutes. Conclusion and Recommendation: The synthesized compound (P5) possessing methoxy group at position-4 of the benzene ring located at position-4 of pyrimidine exhibited good anthelmintic activity. The study revealed the necessity of synthesizing many more compounds with other substituents at position-4 of the benzene ring located at position-4 of pyrimidine.
Keywords: 2-(N, N-dimethyl guanidinyl)-4,6-diaryl pyrimidines, anthelmintic activity, Molinspiration, Osiris, PASS
|How to cite this article:|
Kumarachari RK, Peta S, Surur AS, Mekonnen YT. Synthesis, characterization and in silico biological activity of some 2-(N,N-dimethyl guanidinyl)-4,6-diaryl pyrimidines. J Pharm Bioall Sci 2016;8:181-7
|How to cite this URL:|
Kumarachari RK, Peta S, Surur AS, Mekonnen YT. Synthesis, characterization and in silico biological activity of some 2-(N,N-dimethyl guanidinyl)-4,6-diaryl pyrimidines. J Pharm Bioall Sci [serial online] 2016 [cited 2020 Jul 10];8:181-7. Available from: http://www.jpbsonline.org/text.asp?2016/8/3/181/171678
The biological significance of the pyrimidine derivatives has led us to the synthesis of amino substituted pyrimidines. As pyrimidine is a basic nucleus in DNA and RNA, it has been found to be associated with diverse biological activities. Guanidine readily reacts with β-diketones, β-ketoesters, α, β-unsaturated carbonyl compounds, and cyanoacetic esters to give 2-amino pyrimidines usually in good yields.,, In this study, the nitrogen-containing fragment is metformin (N-C-N fragment guanidine equivalent) and chalcone, generated in situ, serves as an excellent illustrative example in that it readily undergoes a condensation reaction with metformin to produce the title compounds in good yield.
Review of literature reveals that pyrimidine derivatives were reported to possess significant biological activities such as anticonvulsant, antimicrobial, anti-inflammatory, antitumor, and antihistaminic. Recently, our team reported the synthesis, anti-inflammatory and antimicrobial evaluation of some pyrimidines carrying hydroxyl, thiol, phenyl, and amino substituents at the second position.,, In view of these observations and with an aim of continuing our previous work, 2-(N, N-dimethyl guanidinyl)-4,6-diaryl pyrimidines were synthesized and screened for anthelmintic activity. Interestingly, all the 7 compounds exhibited significant anthelmintic activity when compared with the standard.
| Materials and Methods|| |
Melting points of the synthesized compounds were determined in an open capillary tube using digital melting point apparatus and are uncorrected. The purity of the compounds were established by thin layer chromatography using precoated silica gel strips, toluene:chloroform:methanol (5:3:2) as a solvent system and ultraviolet-chamber for detection of spots. Infrared spectra (υ/cm) were recorded on a JASCO FT-IR 4000 (Japan) using KBr disks. CHNO elemental analysis carried by Perkin Elmer Series II 2400 CHNS/O Elemental Analyzer. Mass spectra were obtained on JEOL GC mate II GC- Mass spectrometer at 70ev using direct insertion probe method. Nuclear magnetic resonance (NMR) spectra were taken on BRUKER AVIII-500MHz FT–NMR spectrometer by using tetramethylsilane as internal standard and the solvent used was dimethylsulfoxide.
A chemical reaction could be viewed in two directions: The synthetic direction, corresponding to laboratory operations, and the retro-synthetic direction. This is a problem-solving technique for transforming the structure of a synthetic target molecule to a sequence of progressively simpler structures along a pathway which ultimately leads to simple or commercially available starting materials for a chemical synthesis.
In this procedure, the synthetic target is subjected to a deconstruction or disconnection process which corresponds to the reverse of a synthetic reaction, so as to convert the target structure to simpler precursor structures (synthons) without any assumptions regarding the starting materials. Each of the precursors so generated is then examined, in the same way, and the process is repeated until simple or commercially available structures resulted.
Applying retro-synthetic analysis [Figure 1] on our TGT by disconnecting the two C-N bonds of pyrimidine resulted in α, β-unsaturated carbonyl compound and metformin (N-C-N fragment). Disconnection of isolated double bond in α, β-unsaturated carbonyl compound resulted in aryl aldehydes and aryl methyl ketones.
|Figure 1: The retrosynthetic analysis of 2-(N, N-dimethyl guanidinyl)-4,6-diaryl pyrimidines|
Click here to view
4-Methoxy benzaldehyde, 3, 4, 5-trimethoxy benzaldehyde, acetophenone, 4-methoxy acetophenone, 4-amino acetophenone, 4-methyl acetophenone, 4-hydoxy acetophenone, 4-nitro acetophenone, 4-chloro acetophenone, metformin, methanol, and hydrochloric acid were used to synthesize seven 2-(N, N-dimethyl guanidinyl)-4,6-diaryl pyrimidines.
General procedure to synthesize 2-(N, N-dimethyl guanidinyl)-4,6-diaryl pyrimidines (P1–7)
A solution of aromatic aldehyde (0.01 M), methyl ketone (0.012 M) and metformin ([0.015 M] [N-C-N fragment]) in methanol was refluxed for 12 h in the presence of few drops of concentrated hydrochloric acid as catalyst., The product was isolated through the rotary evaporator and recrystallized using a mixture of water and acetone [Figure 2] (80:20).
|Figure 2: Synthetic scheme of 2-(N, N-dimethyl guanidinyl)-4,6-diaryl pyrimidines (P1-7)|
Click here to view
Prediction of biological activity
Novel pharmacological actions can be found for title compounds on the basis of an online program PASS. Its application to the title compounds was done to identify prospective pharmacological properties that could be confirmed by experimental studies. PASS compares the structure of a new compound with structures of well-known biologically active substance and. Therefore, it is possible to estimate if a new compound may have a particular effect. It operates with many thousands of substances from the training set and provides a more objective estimation. Since only the structural formula of the chemical compound is necessary to obtain PASS predictions, this approach can be used at the earliest stage of the investigation. Structures of the title compounds were drawn through ACD labs Chem sketch software (Canada) submitted to the PASS online program and predicted the possible mechanisms of action as well as biological activities. Among those possible biological activities, the compounds showed more probability to be active for anthelmintic activity.
Molinspiration supports internet chemistry community by offering free on-line services for calculation of important molecular properties such as Molinspiration LogP (mi LogP), polar surface area, number of hydrogen bond donors (HBD), and acceptors and others, as well as prediction of bioactivity score for the most important drug targets such as G protein-coupled receptor (GPCR) ligands, kinase inhibitors, ion channel modulators, enzymes, and nuclear receptors.
Osiris Property Explorer
The Osiris Property Explorer is an integral part of Actelion's in-house substance registration system. It lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid. Prediction results are valued and color coded. Properties with high risks of undesired effects like mutagenicity are shown in red. Whereas a green color indicates drug conform behavior.
The anthelmintic activity was evaluated on adult Indian earthworm Pheretima posthuma due to its anatomical resemblance with the intestinal roundworm parasites of human beings. Nine groups, each containing six earthworms approximately of equal size were used for the study. Each group of earthworms was treated with vehicle (1% CMC), synthesized compounds and standard drug albendazole (100, 200, 500, 1000 μg/ml).
Observations were made for the time taken for paralysis and death of individual worms. Paralysis was said to occur when the worms do not revive even in normal saline. Death was concluded when the worms lost their motility, followed with fading away of their body color.
| Results and Discussion|| |
The title compounds were synthesized according to scheme 1, the physicochemical characterization and structural confirmation (infrared, NMR, mass spectral, and elemental analysis) are presented in [Table 1] and [Table 2]. All the synthesized compounds were obtained as crystalline needles with sharp melting points. The yields of the product were found to be satisfactory. All compounds were in conformity with the structures envisaged.
|Table 1: Structural details and physicochemical properties of synthesized compounds (P1-7)|
Click here to view
|Table 2: Spectral details and IUPAC names of synthesized compounds (P1-7)|
Click here to view
[Table 3] shows the biological activity spectra predicted using PASS computer program. PASS is based on robust analysis of structure – activity relationships in a heterogeneous training set currently including about 60,000 of biologically active compounds from different chemical series with about 4500 types of biological activity. The biological activity types for which the probability to be revealed (Pa) and probability not to be revealed (Pi) are calculated. Pa and Pi values are independent, and their values vary from 0.000 to 1.000. It is reasonable that only those types of activities may be revealed by the compound, where Pa > Pi and so they are put into the biological activity spectrum. If Pa >0.7, the compound is likely to reveal its activity in the experiment, but in this case, the chance of being the analog of the known pharmaceutical agent is high. If Pa <0.5, the compound is unlikely to reveal this activity in the experiment, but if the presence of this activity is confirmed in the experiment, the compound might be a new chemical entity. It is interesting to note that the anthelmintic activity of all the synthesized compounds was predicted as Pa <0.5, and despite this, all of them exhibited significant activity in the experiment.
|Table 3: Predicted biological activity spectrum of synthesized compounds|
Click here to view
Some selected molecular properties were predicted using Molinspiration [Table 4]. All the synthesized compounds were found to obey Lipinski's rule. Molecular weight, Clog P, the number of HBD and acceptors were within the limit. The number of rotatable bonds indicated that all the synthesized compounds are flexible. A number of rotatable bonds is a simple topological parameter and has been shown to be a very good descriptor of oral bioavailability of drugs. Rotatable bond is defined as any single non-ring bond, bounded to nonterminal heavy (i.e. nonhydrogen) atom. Topological polar surface area is a very useful parameter for the prediction of drug transport properties and is defined as a sum of surfaces of polar atoms (usually oxygens, nitrogens, and attached hydrogens) in a molecule. This parameter has been shown to correlate very well with the human intestinal absorption, Caco-2 monolayer's permeability, and blood-brain barrier penetration.
|Table 4: Calculation of molecular properties using Molinspiration v2014.11|
Click here to view
Molinspiration was also used to predict the bioactivity scores of each synthesized compound [Table 5]. All the synthesized compounds scored good bioactivity values as GPCR ligands and kinase inhibitors.
|Table 5: Calculation of bioactivity scores using Molinspiration v2014.03|
Click here to view
Some selected toxicological properties and drug score values were predicted using Osiris Property Explorer [Table 6]. All the synthesized compounds were predicted to be safe regarding toxicity and possessed good drug score values. Drug-likeness may be defined as a complex balance of various molecular properties and structural features which determine whether a particular molecule is similar to the known drugs. These properties, mainly hydrophobicity, electronic distribution, hydrogen bonding characteristics, molecule size, and flexibility and of course presence of various pharmacophoric features influence the behavior of a molecule in a living organism, including bioavailability, transport properties, affinity to proteins, reactivity, toxicity, metabolic stability, and many others.
|Table 6: Predictive toxicity and physico--chemical properties using Osiris molecular property explorer|
Click here to view
All the synthesized pyrimidines were evaluated for anthelmintic activity in P. posthuma at a concentration of 100, 200, 500, and 1000 μg/ml using albendazole as standard reference drug.
All the synthesized compounds (P1-7) were found to exhibit anthelmintic activity. From the [Table 7], it is clear that the compound (P5) was found to be the most potent. Compound (P4) was found to be slightly less potent than (P5), followed by the compounds P3, P1, P2, P7, and P6, respectively. Anthelmintic activity of synthesized compounds in the order of their increasing potency are as follows: compound (P5) > Albendazole > (P4) > (P3) > (P1) > (P2) > (P7) > (P6).
|Table 7: Results of anthelmintic activity of synthesized compounds (P1-7)|
Click here to view
Compound (P5) possess methoxy group at 4th position of the benzene ring located at 4th position of pyrimidine. Compound (P4) possess methoxy group at 4th position of the benzene ring located at 4th position of pyrimidine and hydroxyl group at 4th position of benzene ring located at 6th position of pyrimidine. Compounds (P3, P1, and P2) possess three methoxy groups at 3rd, 4th, and 5th positions of benzene ring located at 4th position of pyrimidine and methyl, methoxy, and amino groups, respectively at 4th position of benzene ring located at 6th position of pyrimidine. Compounds (P7 and P6) possess methoxy group at 4th position of the benzene ring located at 4th position of pyrimidine and chloro and nitro groups, respectively at 4th position of benzene ring located at 6th position of pyrimidine.
The compounds having electron withdrawing groups in the benzene ring located at 6th position of pyrimidine have remarkably less activity than the remaining compounds. From the results, it has been revealed that the compound should have an unsubstituted benzene ring at 6th position of pyrimidine for maximal activity. Mono-substitution on benzene ring located at 4th position of pyrimidine and N, N-dimethyl guanidinyl moiety at 2nd position of pyrimidine seems favorable for anthelmintic activity.
| Conclusion|| |
From the present investigation, it is concluded that we have successfully synthesized the title compounds and evaluated their anthelmintic activity.
The results revealed that the synthesized compound (P5) possessing methoxy group at 4th position of the benzene ring located at 4th position of pyrimidine exhibited good anthelmintic activity. The study revealed the necessity of synthesizing many more compounds with other substituents at 4th position of the benzene ring located at 4th position of pyrimidine. Such compounds may emerge as much more potent anthelmintic agents.
However, further studies are required to establish the mechanism of action of title compounds. The contributing physicochemical properties for the anthelmintic activity need to be established by detailed quantitative structure-activity relationship studies, which may provide insights into the structural requirements of this class of molecules.
Financial support and sponsorship
Conflicts of interest
There are no conflicts of interest.
| References|| |
Ghoneim KM, Youssef R. Synthesis and evaluation of some 2-, 4- and 2,4-disubstituted-6-methylpyrimidine derivatives for antimicrobial activity. J Indian Chem Soc 1986;53:914-7.
Kenner GW, Todd A. Pyrimidine and its derivatives. In: Elderfield RC, editor. Heterocyclic Compounds. New York: Wiley; 1957. p. 6.
Brown DJ. The pyrimidines. In: Weissberger A, editor. The Chemistry of Heterocyclic Compounds. New York: Interscience; 1962. p. 16.
Said A, El-Galil A, Amr E, Sabry NM, Abdulla MM. Analgesic, anticonvulsant and anti-inflammatory activities of some synthesized benzodiazepine, triazolopyrimidine and bisimide derivatives. Eur J Med Chem 2009;44:4787-92.
Habib NS, Soliman R, El-Tombary AA, El-Hawash SA, Shaaban OG. Synthesis of thiazolo[4,5-d] pyrimidine derivatives as potential antimicrobial agents. Arch Pharm Res 2007;30:1511-20.
Kamble RR, Sudha BS. Synthesis and pharmacological screening of 5-methyl -3- [P-(6'-aryl-2'-thioxo- 1',2',5'6'-tetrahydro-pyrimidin- 4-yl)-phenyl]-3H-2-oxo-D4-1,3,4- oxadiazoles. Indian J Pharm Sci 2006;68:249-53.
Naik TA, Chikhalia KH. Studies on synthesis of pyrimidine derivatives and their pharmacological evaluation. Eur J Med Chem 2007;4:60-6.
Rahaman SA, Rajendra Pasad Y, Kumar P, Kumar B. Synthesis and anti-histaminic activity of some novel pyrimidines. Saudi Pharm J 2009;17:255-8.
Rajendra Prasad Y, Rajasekhar KK, Shankarananth V, Maulali SC, Pradeepkumar GS, Narender Reddy K. Synthesis and antimicrobial activity of some substituted pyrimidine derivatives. J Pharm Res 2010;3:2291-2.
Rajendra Prasad Y, Rajasekhar KK, Shankarananth V, Narender Reddy K, Pradeepkumar GS, Nagendrababu N. Synthesis, antiinflammatory and antimicrobial evaluation of 2-phenyl- 4,6-diaryl substituted pyrimidine derivatives. J Pharm Res 2010;3:2480-2.
Rajendra Prasad Y, Rajasekhar KK, Shankarananth V, Pradeepkumar GS, Narender Reddy K, Vijaykumar N. Synthesis and biological evaluation of 2-amino-4,6-diaryl substituted pyrimidine derivatives. J Pharm Res 2010;3:2631-3.
Deshmukh MB, Anbhule PV, Jagtap SS, Patil DR, Salunkha SM. A novel and environmental friendly, one-step synthesi of 2,6-Diamino-4-phenyl pyrimidine-5-carbonitrile using potassium carbonate in water. Indian J Chem Sec B 2008;47B:792-5.
Joule JA, Mills K. The diazines: pyridazine, pyrimidine and pyrazine: reactions and synthesis. Heterocycl Chem 2009;4:218-20.
. [Last accessed on 2014 Jun 15].
Ertl P, Rohde B, Selzer P. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J Med Chem 2000;43:3714-7.
Sander T. Actelion's property explorer. Allschwil, Switzerland: Actelion's Pharmaceuticals Ltd.; 2001.
Deore SL, Khadabadi SS, Kamdi KS. In vitro
anthelmintic activity of Cassia tora
. Int J Chem Tech Res 2009;1:177-9.
[Figure 1], [Figure 2]
[Table 1], [Table 2], [Table 3], [Table 4], [Table 5], [Table 6], [Table 7]