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.
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