Target Oriented Selective Synthesis of Antibacterial Active Tyrosinase Enzyme Inhibitor Coumarin Core Derivatives

 

Digambar Kumbhar1, Reshma Patil1, Dayanand Patil2, Ajinkya Patravale2,

Dattatray Chandam2, Sunetra Jadhav1, Dattatray Chavan2, Prafulla Choudhari3,

Manish Bhatia3, Madhukar Deshmukh1,2*

1Department of Agrochemicals and Pest Management, Shivaji University, Kolhapur, M.S., India

2Department of Chemistry, Shivaji University, Kolhapur, M.S., India

3Computational Drug Discovery Lab Department of Pharmaceutical Chemistry Bharati Vidyapeeth College of Pharmacy, Kolhapur, M.S., India

*Corresponding Author E-mail: shubhlaxmi111@gmail.com

 

ABSTRACT:

Target oriented designs and selective synthesis of bioactive molecules with broad spectrum activity is a challenging job in the field of modern organic chemistry. Considering this opportunity herein, we report a highly competent selective synthesis of bioactive coumarin core derivative. Using computational drug design software only four selective antibacterial active derivatives was discovered and then synthesized. The efficiency of the synthesized compounds was scrutinized against bacterial pathogens such as P. vulgaris and B. megaterium. All the synthesized compounds showed better theoretical as well as practical results against selected pathogenic species. The minimum inhibitory concentration (MIC) values of the most active heterocycles were compared with that of ciprofloxacin. Results obtained in tyrocinase inhibition assay exactly correlate with MIC results and docking outcomes. The bioactivity of these type moieties provided a novel approach to develop new types of antibacterial drugs like entities effective against pathogens.

 

KEYWORDS: Docking simulation; Coumarin aldehyde; Cyclic 1, 3- diketone ; Acetic acid medium; Antibacterial activity; MIC, Tyrocinase inhibition assay.

 

 


INTRODUCTION:

Efficient diseases control, design and synthesis of broad spectrum bioactive novel molecule having potent capacity to solve problems in front of human being and agricultural sectors are greatly necessitating.1 Recently a multiple antibiotic resistance increasing in pathogens and spread serious diseases in the society. Hence, there is a great inevitability to develop new types of antimicrobial agents.1

 

 

Fig. 1 Structural resemblance with some marketed drugs.

 

 

Target oriented synthesis of novel drug like molecule scrutinized from divers skeletal motifs was developed by using Diversity-oriented synthesis (DOS) approach is the emerging aspects in medicinal chemistry. DOS populates chemical space broadly with small-molecules having diverse structures.2 DOS includes the development of pathways most important to efficient synthesis of collections of small molecules having skeletal and stereochemical diversity.2,3 Designed compounds have fused scaffold incorporated in coumarin, pyrimidine, carboxamide groups and pyranocoumarin motifs are of the great biological interest4 due to their biological activities such as antimicrobial,5,6 anticoagulant,7,8 antioxidant,9,10 anticancer,11,12 choline esterase inhibitor14 etc. The diversity oreanted multicamponant reactions produce highly variable bioactive motifs having potential to act as a antifungal, anti tuberculosis, anti oxidant, anticancer, antibacterial drug like molecule.

 


 

Fig. 2 Design coumarin core structures and screen over docking software.

 


 

In this concern enzyme inhibition study was predicted by using computational drug design methods. In the search of antibacterial active potent molecule was forecast by using perfect binding ability with suitable enzyme in the test organisms such as tyrosinase enzyme. Enzyme tyrosinase are important enzymes in the bacteria plays important cell functions. Occurrence of this enzyme in many bacterial species. The drug active against this type of enzyme inhibition resulted better prevention of pathogenic species.

 

Literature surveys show that these types of moieties are used as drugs in the market such as warfarine, coumatetralyl, uvafzlelin [Fig. 1] etc. Hence, it is possible that the fused scaffolds of coumarin with 1, 3 diketone have potential to act novel drugs. With this, herein we reported a simple and an efficient synthesis of some coumarine derivatives and to study their bioefficiency. Here, we report development of target orientated synthesis of the novel coumarin derivatives with antimicrobial activity and their virtual analysis to ascertain the mode of action.

 

RESULTS AND DISCUSSION:

At the beginning of the scheme, we firstly illustrate the different types of structures having different functional groups by varying reactants with common coumarin core [fig. 2].

 

Then these structures are screened over docking software with selective enzymes like tyrocinase, beta lactames etc. Out of this enzyme tyrosinase are important enzymes in the bacteria shows importance in other cell related functions also playing vital role in the biosynthesis of melanin and signal transmissions in cell. Due to occurrence of the tyrosinase in large number of bacteria so inhibition of tyrosinase can act as useful tool for the broad spectrum antibacterial design. The docking analysis is utilized to ascertain the mode of action of synthesized derivatives.

 

Docking analysis of Tyrosinase (PDB ID 3NQ1)

All the designed molecules were docked in the similar binding site having binding energies ranging from -63.24 kcal/ mol to -23.24 kcal/mol out of 14 synthesized derivatives the 3a, 3b exhibited profound antibacterial activity. The barbituric acid and thio-barbituric acid containing derivatives E, D respectively (Fig. 2) are more potent in biological assay. In the virtual analysis these molecules showed significant interaction than other designed derivatives. Da (Scheme 1) exhibited hydrogen bonding interaction with GLY196 (2.5 Ǻ) and ARG 209 (2 Ǻ) and hydrophobic interactions with LYS276 and SER237A, also number of vander wall interactions were observed with amino acids like PRO201, ARG209, ARG209, GLY196, LYS 276, SER 237A with total binding energy of    -67.29 kcal/ mol. Db is other active derivative sulphur containing pyrimidine and it is also active in biological assay. Db (Scheme 1) showed hydrogen bond interaction with ARG209 (2.3 Ǻ), hydrophobic interaction with PRO201, ARG209 and total binding energy of -61.1 kcal/mol. The barbituric acid containing derivatives 3c and 3d are also found to be equally active to that of thiobarbituric acid enclosing derivatives Da and Db. Molecule Ea (Scheme 1) showed hydrogen bond interaction with ASN205 (2.4 Ǻ) and aromatic interaction with HIS208 (4.5 Ǻ) while the another barbituric acid derivative Eb (Scheme 1)  lacks in aromatic interaction but showed hydrogen bond interaction with ARG209 and two hydrophobic interaction with ARG209 and PRO201. The results of the virtual analysis indicated the synthesized derivatives were showed antibacterial activity via inhibition of tyrosinase [Fig 3].


 

Fig. 3 Shows all significant interaction of the molecules with tyrosinase enzyme (a) Interaction of Da with tyrosinase (b) Interaction of Db with tyrosinase (c) Interaction of Ea with tyrosinase (d) Interaction of Eb with tyrosinase.

 

 

 


We observed excellent binding energy and good binding interactions with selected bacterial enzymes. These results encourage us to synthesize those types of biological active moieties having high potential to act as new microbial drug like molecules.

 

In our exploratory experiments, we investigate the mixture of coumarin aldehydes (1 mmol) and 1, 3- diketone, (thiobarbituric acid (2 mmol), barbituric acid (1 mmol)) added in a 25 ml round bottom flask containing 5 ml ethanol: acetic acid (1:1) and the mixture was filtered wash with water, then with diethyl either to get targeted compounds which was recrystallized to get desired product. The synthetic pathway for the targeted compounds Da, Db, Ea and Eb was illustrated in scheme 1.


 

 

Scheme 1: Synthesis of selective antibacterial active coumarin derivatives


 

 


The plausible mechanism of the product formation is depicted in figure 4. In acidic medium, electrophilic activation of aldehyde 1 and subsequent attack of 1, 3-cyclic active methylene  compound 2 gives the Knoevenagel intermediate which further upon the nucleophilic attack of another molecule of 1, 3-cyclic active methylene compound 2 followed by cyclization afforded a series of coumarin derivatives [Fig 4].


 

Fig. 4 Synthetic route of targeted compounds.

 

 


With these results in our hands, we then investigated the diversity of our protocol using various 1,3-diketone and coumarin aldehyde under optimized condition. To our surprise, cyclic 1, 3-diketone such as thiobarbituric acid (2a) underwent reaction smoothly to afford excellent yield of the respective products (entry Da-Db, Table 1). In case of Barbituric acid (2b) the reaction extruded knoevenagel adducts as products (entry Ea-Eb, Table 1). These observations showed divers reactivity of different types of cyclic 1, 3-diketones with coumarin aldehydes to give up diverse types of compounds having different functional groups.


 

 

Table 1. Physical data of targeted compounds.

 


Biological activity

All the synthesized compounds were screened against the gram positive Bacillus megaterium and gram negative Proteus vulgaris species. Antibacterial activity was carried out by broth dilution method using ciprofloxacin as a standard. At first all the compounds were tested make final concentration of 10, 25, 50, 75 and 100 μg/ml. The results shows that 75, 50, 50 and 50 μg/ml concentrations of compounds 3a, 3b, 3c and 3d effective against gram positive Bacillus megaterium  species respectively (Table 3, Fig. 5). Moreover, 50, 50, 50 and 50 μg/ml concentrations of the compounds 3a, 3b, 3c and 3d also shows excellent inhibition of gram negative Proteus vulgaris species respectively (Table 3, Fig. 5).

 

The lead compounds (3a, 3b, 3c and 3d) are further tested with tyrosinase enzyme using kojic acid and ascorbic acid as a standard. Results obtained in tyrosinase inhibition bioassay exactly coordinate with MIC results and docking results (Fig. 6). Thus, antibacterial activity of the synthesized derivatives indicated that the presence of sulphur containing pyrimidine played predominant role in exhibiting the biological activity of the molecules, sulphur and both the nitrogen on the thiobarbituric acid was bind coordinately with  hydrogen which can increase the binding potential of the molecules with microbial enzymes. The barbituric acid influences the binding potential of the molecules due to presence of two amino groups contributing for hydrogen bond interactions with the receptor which are clearly indicated in the docking studies. Other derivatives also showed activity but these compounds are relatively less potent with respect to the compounds described previously.

 

Prediction of ADME properties

Pharmacokinetic behavior of the molecules were predicted using the lipinsky rule of five different parameters which regulates the kinetic faith of the molecules are calculated using molinsiron server and V life MDS 4.3 all the molecules follows the lipinsky rule  which indicates the good drug like properties of the molecules [Table 2]

 


 

 

Table 2. Pharmacokinetic behavior of the synthesized molecules.

Molecules

Hydrogen Bond Acceptor Count

Hydrogen Bond Donor Count

Rotatable Bond Count

Molecular Weight of compounds

log p

TPSA

(%) Absorption

Da

5

4

1

426.4

0.2237

136.7

61.83

Db

6

4

1

444.4

0.3629

136.7

61.83

Ea

4

2

1

284.2

0.438

113

70.01

Eb

5

2

1

302.2

0.5771

113

70.01

 

 


CONCLUSION:

In the summary, we have synthesized novel coumarin derivatives, and their antibacterial activity was evaluated. The reaction was forwarded efficiently by using Ethanol: Acetic acid (1:1) was used for the preparation of coumarine derivatives under reflux conditions. The attractive features of this protocol are the simple procedure, cleaner reaction and use of economical solvents. Satisfactory yields of products, simple reaction, isolation and purification of the products make it a best protocol for these classes of compounds. Among all of the compounds verified potent inhibition proved by theoretically as well as practically against both the tested strains. 3a, 3b, 3c and 3d exhibited profound antibacterial activity against the both the species also confirm by docking study, MIC study and tyrosine inhibition study. This report proves that coumarin fused with pyrimidine motifs possess stronger bactericidal activity. The importance of this work might be more effective drugs against pathogens, which could be supportive in synthesis of most powerful drugs entities for treatment of various infections.

 

MATERIALS AND METHODES:

All chemicals were used commercially available and purchased from Sigma Aldrich. Melting points were taken on a melting point apparatus and are uncorrected. The reactions were monitored by thin layer chromatography (TLC). Proton nuclear magnetic resonance (1H NMR) and 13C NMR spectra were recorded on a Bruker DPX 300 MHz/ 75 MHz frequincies, respectively using DMSO d6  as a solvent and tetramethylsilane (TMS) as an internal standard. Infrared (IR) spectra were recorded on a Perkin Elmer spectrum 100 and JASCO, FTIR 4600 spectrophotometer. Mass spectra were recorded on a Shimadzu mass spectrophotometer. Elemental analysis was done on a Flash elemental analyzer EURO EA-3000. Biological assay was carried out using nutrient broth method. The solutions were prepared by using DMSO as a solvent. MIC values of the compounds were recorded by broth dilution method using Naanolab Autoclave, Laminar flow and Incubator. Tyrosinase bioassay results were recorded on Chemito UV-Visible 2100 spectrophotometer. The pre-incubation with enzyme consisted of a phosphoric acid buffer solution (pH 6.8, 1.8 mL), an aqueous solution of mushroom tyrosinase (1000 U/ml, Sigma Chemical Co., 0.1 ml) and DMSO (0.1 ml) with or without an added sample.

 

Virtual Screening

To ascertain the mode of action of these derivatives the virtual analysis of the developed molecules were carried out using biopredicta module of the V life MDS 4.3. Protein structures were downloaded from the www.rcsb.org. The protein structures were optimized by keeping the hydrogen atoms and removing water molecules from the protein. Virtual analyses of the molecules were carried out keeping ligand flexible, 10000 conformation of the each synthesized derivative were prepared and utilsed for the docking analysis. The best fitted 100 conformation were selected based on the binding energy, these structures were further analyzed for the interaction potential of the molecules.  Virtual analyses of the synthesized derivatives were carried out on protein targets bacterial tyrosinase (PDB ID 3NQ1). All dockings were taken into 1 million energy evaluations were performed for each of the synthesized molecules. Docked ligand conformations were analyzed in terms of energy and interaction between ligand and receptor proteins. A computational study of synthesized compounds was performed via calculations of ADME properties. Polar surface area (TPSA), Log P, number of rotatable bonds, molecular volume, number of hydrogen donor and acceptor atoms and violations of Lipinski’s rule of five were calculated using Molinspiration online property calculation toolkit and V life MDS 4.3.17,18 Absorption (% ABS) was calculated by % ABS = 109 X (0.345 TPSA).19,20

 

General procedure for the syntheses of compounds [3a-3d]

In a 25 ml round-bottom flask coumarin aldehyde 1 (1 mmol) and cyclic 1, 3 diketone compounds 2 (2 mmol) went in 10 ml of ethanol: acetic acid (1:1). Reaction mixture was stirred for appropriate time at reflux condition after 80 to 120 min. solid separates and completion of the reaction monitored by TLC. Then the reaction mixture cooled and separated solid filtered wash with water, then with hot ethanol and diethyl ether further purified by recrystalization from EtOH mixture to give a targeted compound 3a-3d in 70-75% yield (Table 1).

 

5- (4-Oxo-4H-chromen-3-yl)- 2, 8 -dithioxo-2, 3, 5, 7, 8, 9 - hexahydro-1H-pyrano[2, 3-d;6, 5-d] dipyrimidine-4, 6-dione (Da)

Orange color powder; yield 72 %; mp 280-282° C, IR (ν max / cm-1): 3054, 2904, 1656, 1577, 1510, 1460, 1418, 1360, 1311, 1246, 1190, 1153, 1000 cm-1 ; 1H NMR (300 MHz; DMSO - d6; Me4Si): δ, 5.772 (s, 1H), 7.432-7.559 (m, 1H), 7.714-7.742 (m, 1H), 7.766-7.772 (d, 2H), 8.114-8.146 (m, 1H), 8.638 (s, 1H), 9.897 (s, 1H), 11.185 (s, 1H), 11.374 (s, 1H) ppm; 13C NMR (75 MHz; DMSO - d6 ; Me4Si):  δ, 24.96, 117.67, 118.24, 119.08, 120.29, 123.11, 123.55, 125.11, 125.49, 125.74, 126.99, 133.67, 135.48, 153.72, 156.09, 163.29, 173.02, 176.75, 188.69 ppm; anal. calcd. found C, 50.45; H, 2.20; N, 13.30 %; C18H10N4O5S2 ; requires C, 50.70; H, 2.36; N , 13.14 %.

 

5 - (6-Fluoro-4-oxo-4H-chromen-3-yl) - 2, 8-dithioxo-2, 3, 5, 7, 8, 9 - hexahydro-1H-pyrano[2, 3-d;6, 5-d’]dipyrimidine-4, 6-dione (Db)

Orange color powder; yield 75 %; mp 232-234° C, IR (ν max / cm-1): 3074, 2922, 1661, 1512, 1460, 1360, 1310, 1191 cm-1 ; 1H NMR (300 MHz; DMSO - d6; Me4Si): δ, 5.742 (s, 1H), 7.566 -7.687 (m, 4H), 8.055 (s, 1H), 8.157 (s, 1H), 11.716 (s, 1H), 12.014 (s, 1H) ppm; 13C NMR (75 MHz; DMSO - d6 ; Me4Si):  δ, 117.78, 119.39, 120.00, 120.45, 123.47, 125.11, 125.78, 126.17, 127.24, 135.73, 145.64, 155.74, 156.08, 160.68, 161.72, 162.97, 164.06, 175.11, 175.41, 176.36, 178.97, 188.91 ppm; anal. calcd. found C, 48.44; H, 2.24; N, 12.42 %; C18H9FN4O5S2;  requires C, 48.65;  H, 2.04,  N, 12.61%.

 

5-(4-Oxo-4H-chromen-3-ylmethylene)-pyrimidine-2, 4, 6-trione (Ea)

Yellow color powder; yield 72 %; mp 288-290° C, IR (ν max / cm-1): 3238, 3086, 2829, 1683, 1630, 1537, 1463, 1346, 1311, 1220, 1192 cm-1 ; 1H NMR (300 MHz; DMSO - d6; Me4Si): δ, 7.465-7.515 (t, 1H, J = 7.8 Hz), 7.586-7.614 (d, 1H, J = 9 Hz), 7.760-7.812 (t, 1H, J = 7.2 Hz), 7.971 (s, 1H), 8.121 -8.147 (d, 1H, J = 7.8 Hz), 8.58 (s, 1H), 9.88 (s, 1H), 11.36 (s, 1H), 11.43 (s, 1H) ppm; 13C NMR (75 MHz; DMSO - d6 ; Me4Si): δ, 21.22, 117.58, 118.79, 123.51, 126.19, 126.65, 133.31, 135.00, 146.27, 150.32, 155.71, 162.78, 163.20, 164.15, 175.32 ppm; Mass (m/z): 312 (M+); anal. calcd. found C, 59.38; H, 2.58; N, 9.66 %; C14H8N2O5; requires C, 59.16;  H, 2.84;  N , 9.86 %.

 

5-(6-Fluoro-4-oxo-4H-chromen-3-ylmethylene)-pyrimidine-2,4,6-trione (Eb)

Yellow color powder; yield 70 %; mp 308-310° C, IR (ν max / cm-1): 3242, 3097, 1769, 1674, 1548, 1482, 1435, 1315, 1221 cm-1 ; 1H NMR (300 MHz; DMSO - d6; Me4Si): δ, 7.664 – 7.691 (t, 1H, J = 6 Hz), 7.745 -7.806 (m, 2H), 8.119 (s, 1H), 8.498 (s, 1H), 9.829 (s, 1H), 11.392 (s, 1H), 11.474 (s, 1H) ppm; 13C NMR (75 MHz; DMSO - d6 ; Me4Si): 117.06, 120.29, 122.26, 123.42, 123.74, 124.84, 144.43, 150.55, 152.27, 158.38, 162.76, 163.37, 163.53, 170.27, 174.66 ppm; anal. calcd. found C, 55.48; H, 2.54; N, 9.12 %; C14H7FN2O5 ; requires C, 55.64; H, 2.33; N , 9.27 %.

 

Biological assay

For antibacterial screening gram positive Bacillus megaterium and gram negative Proteus vulgaris were chosen procured from the Department of Microbiology, Shivaji University, Kolhapur. The synthesized entire compounds were tested for their antimicrobial activity against gram +ve and gram –ve pathogenic bacterial strains.

 

In-vitro Antibacterial Activity 23-28

Gram-positive bacteria Bacillus megaterium and Gram-negative Proteus vulgaris were used against standard Ciprofloxacin. MICs (μg/ml) were determined by a broth method as recommended by the NCCLS.24 The results were summarized in [Table 3 and Fig. 5].

 

 

 

Table 3. MIC of Synthesized compounds.

 

Comp.

Antibacterial activity (µg/ml)

Bacillus megaterium

(gram + ve)

Proteus vulgaris

(gram - ve)

Da

75

50

Db

50

50

Ea

50

50

Eb

50

50

ciprofloxacin

25

10

 


 

Fig. 5 The graph shows minimum inhibitory concentration (MIC) of synthesized compounds against bacterial species.


 

 


Fig. 6 The graph shows percentage inhibition of enzyme tyrosinase.

 

 


In-Vitro Tyrosinase Inhibitory Assay

Tyrosinase activity assays were performed with L-DOPA as substrate, as previously described.29,30   Results are recapitulated in fig. 6.

 

ACKNOWLEDGMENT:

One of the author’s thanks the University Grand Commission (UGC) for awarding NET-JRF fellowship and the Department of Chemistry, Shivaji University, Kolhapur for providing NMR and IR screening facilities. We are gratefully acknowledged the molinspiration website and Department of Bio-Technology, Shivaji University, Kolhapur for offering tyrosinase enzyme assay.

 

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Received on 25.06.2015         Modified on 13.07.2015

Accepted on 23.07.2015        © AJRC All right reserved

Asian J. Research Chem. 8(8): August 2015; Page 511-520

DOI: 10.5958/0974-4150.2015.00081.4