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Available online at www.worldscientificnews.com
( Received 23 December 2018; Accepted 10 January 2019; Date of Publication 11 January 2019 )
WSN 118 (2019) 100-114 EISSN 2392-2192
Synthesis, characterization and docking studies of some novel xanthene derivatives
Aditya H. Bhatt1,*, Viral R. Shah1, Rakesh M. Rawal2
1Department of Chemistry, Kamani Science & Prataprai Arts College, Amreli, Gujarat, India
2Department of Life Sciences, Gujarat University, Ahmedabad, Gujarat, India
*E-mail address: bhattaditya88@gmail.com
ABSTRACT
The synthesis of a novel xanthene derivatives bearing dimedone as an excellent precursor has
been achieved by applying one pot three component Hantzsch type condensation. The newly synthesized
compounds were characterized by spectral and elemental analyses. All synthesized compounds undergo
docking studies and biological screening for antimicrobial activity against Gram-positive bacteria,
Gram-negative bacteria and fungal species. Among all the tested compounds, it was found that
compound 3c, 3d, 3g and 3h revealed better activities against the Gram-positive rather than the Gram-
negative bacteria whereas results of docking studies revealed that compounds 3b, 3g and 3i showed best
binding affinity towards ATP binding pocket of Human PIM1 kinase receptor through steric favorable
and H-bond interactions.
Keywords: Xanthene, Hantzsch synthesis, Antimicrobial activity, Docking studies
1. INTRODUCTION
Dimedone is an alicyclic compound having 1,3-dicarbonyl groups flanked by a methylene
group and exists in a tautomeric trans-enolized form where intramolecular hydrogen bonding
is not possible 1. The inherent structural features of dimedone have created various reactive
centers: C-1, C-2, and to a less extent C-6 in addition to C-3 or 3-O. Moreover, dimedone is an
excellent precursor for partially hydrogenated fused heterocycles 2, where two of the carbon-
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atoms of dimedone are part of the back bone of the formed heterocycles. Its structural features
and its reactivity to form more functionalized derivatives have led to the construction of a wide
range of fused or spiral biheterocycles.
Xanthenes are frequently occurring motifs in a number of natural products 3 and have
been used as versatile synthons due to the inherent reactivity of the inbuilt Pyran ring 4. Most
of the natural schweinfurthins 5 (diversonol and blennolide C) are potent and selective inhibitors
of cell growths measured by the National Cancer Institute’s 60-cell line screen 6. Xanthenes
and xanthene derivatives exhibit anti-cancer 7, anti-oxidant8, anti-inflammatory and potential
analgesic activities 9. Xanthenes are rare in natural plants; most of them are synthesized or arise
as a microbial metabolite. Xanthenes are also known for their utility as leuco-dyes 10, pH
sensitive fluorescent materials for the visualization of biomolecules 11 and in laser technologies 12 due to their useful spectroscopic properties.
Despite continued research efforts towards the development of anticancer drugs, cancer
remains a primary cause of death. It is estimated that the number of cancer cases may reach up
to 15 million at the end of 2020 13-17. It is well established that small heterocyclic molecules are
predominant building blocks for biologically active compounds 18,19. Xanthenes are important
structural units found widely in natural products. Molecular scaffolds of xanthene are important
as PIM1 kinase inhibitors. Epicalyxin F is the most potent member of this class, as an anticancer
agent against human HT-1080 fibrosarcoma and murine 26-L5 carcinoma20.
PIM1 oncogene in humans is a type of serine/threonine-protein kinase. The PIM1
oncogene was first exemplified in context to murine T-cell lymphomas, as it was most
commonly activated by the murine leukemia virus. Subsequently, the oncogene has been
associated in multiple human cancers, including acute myeloid leukemia, prostate cancer, and
other hematopoietic malignancies. Mostly it is expressed in bone marrow, prostate, spleen and
thymus, oral epithelial and fetal liver cells. PIM1 oncogene is found to be highly expressed in
cell cultures isolated from human tumors. PIM1 is mainly involved in cell cycle progression,
apoptosis and transcriptional activation, as well as more general signal transduction pathways 21 . Synthesis of 1,8-dioxo-octahydroxanthene is generally achieved by the condensation of 5,5-
dimethyl-1,3-cyclohexanedione with aromatic aldehyde using Lewis acid catalysts such as p-
dodecylbenzenesulfonic acid 22, diammonium hydrogen phosphate 23, silica gel supported ferric
chloride 24, Dowex-50W 25, polyethylene glycol 26-29.
In view of these observations and with a view to further assess the pharmacological
profile of this class of compounds; a novel series of Xanthenes (3a-3j) are synthesized. The
synthesis of polyhydroxanthene-1,8-diones (3a-3j) was achieved by one pot reaction of two
moles of 5,5-dimethylcyclohexane-1,3-dione (dimedone) with one mole of substituted 3-(aryl)-
1-phenyl-1H-pyrazole-4-carbaldehyde in presence of piperidine. The products were
characterized by FT-IR, 1H NMR, 13C NMR spectroscopy and elemental analyses. The newly
synthesized compounds were subjected to antimicrobial activity and docking studies 27-29.
2. EXPERIMENTAL
2. 1. Materials and methods
All research chemicals for the reactions were purchased from Sigma–Aldrich Ltd.,
Merck, and Spectrochem. Melting points were taken in open capillary method and are
uncorrected. IR spectra were recorded on Shimadzu FTIR-8400 spectrophotometer, using KBr
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pellet method.1H-NMR and 13C-NMR spectra of the synthesized compounds were recorded on
a Bruker-Avance-III (400 MHz) DMSO-d6 solvent. Chemical shifts are expressed in δ ppm
downfield from TMS as an internal standard. Mass spectra were determined using direct inlet
probe on a Shimadzu GCMS-QP 2010 mass spectrometer. The purity of the compounds was
checked by thin layer chromatography (TLC) GF254 silica gel plates from E-Merck Co. using
Hexane: Ethyl acetate as eluent and spots were detected in UV.
2. 2. Synthetic route
Table 1. Synthesized molecular scaffolds.
Entry R1
3a 4-OCH3
3b 3-OCH3
3c 4-Br
3d 4-Cl
3e 4-CH3
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3f 4-CH3
3g 3-NO2
3h 3-Br
3i 2-OH
3j 4-OH
General procedure for synthesis of compounds 3-(aryl)-1-phenyl-1H-pyrazole-4-
carbaldehydes (2)
Synthesis of 3-(aryl)-1-phenyl-1H-pyrazole-4-carbaldehydes was achieved by reported
method27.
General procedure for synthesis of 9-(3-(aryl)-1-phenyl-1H-pyrazol-4-yl)-3,3,6,6-
tetramethyl-3,4,5,6,7,9-hexahydro-1H-xanthene-1,8(2H)-dione (3a-3j)
A mixture of the 5,5-dimethylcyclohexane-1,3-dione (dimedone) (0.02 mol) (1) and 3-
(aryl)-1-phenyl-1H-pyrazole-4-carbaldehyde (0.01 mol) (2a-2j) in presence of piperidine (2-3
drops) was refluxed in ethanol as a solvent at 60-80 ºC for 4-6 hrs. The progress of the reaction
was monitored by TLC. Upon completion of the reaction, the reaction mass was poured into
ice-cold water, the product was filtered, washed with water, dried and crystallized from ethanol-
DMF (9:1) mixture.
2. 3. Molecular docking studies
Molecular docking is an important tool which predicts the extended orientation by
showing the interactions between ligand and the protein and the aim is to achieve an optimized
conformation for both the protein and the ligand and the relative orientation obtained should be
such that the free energy of the overall system should be decreased. Molecular docking studies
have been carried out with series of xanthene derivatives which are potent and highly selective
PIM1 kinase inhibitors. All the structures of synthesized derivatives were drawn using
Chemdraw software. We have carried out ligand based molecular docking using Molegro
Virtual Docker 6.0 (MVD) software to identify the binding modes of synthesized derivatives
required for the potential anticancer activity. The crystal structure of protein was downloaded
from RCSB protein data bank (PDB ID: 1XQZ).
The database of molecular docking study consisted of 1XQZ with 10 ligand molecules.
Docking studies of the title compounds was done on MVD using grid-based docking method.
The crystal structure of 1XQZ obtained from protein data bank was further used for docking
purpose by removing water molecule. The 2D structures of the compounds were built and then
converted into 3D structures. The cavities in the receptor were mapped to assign an appropriate
active site. All the cavities present in receptor were identified and ranked based on their size
and hydrophobic surface area. Finally, ligand molecules were docked into the active site of
receptor to check their interactions. Results of molecular docking study are tabulated in Table
3.
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2. 4. In vitro antimicrobial activity
All of the synthesized compounds (3a-3j) were tested for their antibacterial and antifungal
activity (MIC) in vitro by broth dilution method 28,29 with two Gram-positive bacteria
Staphylococcus aureus MTCC 96, Streptococcus pyogenes MTCC 443, two Gram-negative
bacteria Escherichia coli MTCC 442, Pseudomonas aeruginosa MTCC 441 and three fungal
strains Candida albicans MTCC 227, Aspergillus Niger MTCC 282, Aspergillus clavatus
MTCC 1323 taking ampicillin, chloramphenicol, ciprofloxacin, nystatin and griseofulvin as
standard drugs. The standard strains were procured from the Microbial Type Culture Collection
(MTCC) and Gene Bank, Institute of Microbial Technology, Chandigarh, India.
The minimal inhibitory concentration (MIC) values for all the newly synthesized
compounds were determined by using broth micro dilution method according to NCCLS
standards. MIC value is defined as the lowest concentration of the compound preventing the
visible growth. Serial dilutions of the test compounds and reference drugs were prepared in
Mueller-Hinton agar. Drugs (10 mg) were dissolved in dimethylsulfoxide (DMSO, 1 mL).
Further progressive dilutions with melted Mueller-Hinton agar were performed to obtain the
required concentrations of 1.56, 3.12, 6.25, 10, 12.5, 25, 50, 62.5, 100, 125, 250, 500 and 1000
µg mL-1. The tubes were inoculated with 108 cfu mL-1 (colony forming unit/mL) and incubated
at 37 ºC for 24 h. The MIC was the lowest concentration of the tested compound that yields no
visible growth (turbidity) on the plate. To ensure that the solvent had no effect on the bacterial
growth, a control was performed with the test medium supplemented with DMSO at the same
dilutions as used in the experiments and it was observed that DMSO had no effect on the
microorganisms in the concentrations studied.
Fungal species were employed for testing antifungal activity using cup-plate method. The
culture was maintained in Sabouraud's agar slants. Sterilized Sabouraud's agar medium was
inoculated with 72h old 0.5 ml suspension of fungal spores in a separate flask. About 25 ml of
the inoculated medium was evenly spreaded on a sterilized petridish and allowed to set for 2h.
The cups (10 mm in diameter) were punched in petridish and loaded with 0.5 ml of (0.5 mg/mL)
solution of sample in DMF. The plates were inoculated at 30 °C for 48h. After the completion
of inoculation period the zone of inhibition of growth in form of diameter was measured in mm.
Along with the test solution in each petridish one cup was filled with solvent which acts as
control. The control was maintained with 0.05 ml of DMSO in similar manner. The results
obtained from antimicrobial susceptibility testing are depicted in Table 2.
3. RESULT AND DISCUSSION
3. 1. Analytical data
Structures of the synthesized compounds were characterized by IR, 1H NMR, 13C NMR
and Mass spectroscopic technique. In IR spectra, Confirmatory bands for carbonyl group, C-H
asymmetrical and symmetrical stretching bands of methyl groups were observed at 1645 cm-1,
2943 cm-1 and 2847 cm-1 respectively. In 1H NMR spectra, characteristic singlet and multiplet
were observed for methyl (-CH3) and methylene (-CH2) groups at 0.90-0.99 δ ppm and 1.96-
2.50 δ ppm respectively. Confirmatory signal of methane (-CH) proton was observed at 4.91 δ
ppm. In 13C NMR spectrum signal of carbon of pyran ring was observed in the region of 154-
160 δ ppm whereas signal for carbonyl carbon of dimedone observed at 190-200 δ ppm.
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9-(3-(4-methoxyphenyl)-1-phenyl-1H-pyrazol-4-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-
hexahydro-1H-xanthene-1,8(2H)-dione (3a)
Yield: 72%; pale yellow solid; m.p: 154–156 °C; IR (KBr, cm-1): 3052, 2857, 2886, 1716,
1622, 1597; 1H NMR (DMSO d6, 400 MHz) δ: 0.902 (s, 6H, CH3); 0.988 (s, 6H, CH3); 3.82
(s, 3H, OCH3); 4.97 (s, 1H, C-H) 7.44 (s, 1H, Ar–H); 8.10 (s, 1H, CH); 13C NMR (DMSO d6,
400 MHz) δ: 28.62 (CH3, C-1); 32.06 (C(CH3)2, C-2); 117.67 (C-6); 129.40 (Ar–CH, C-10);
139.52 (Ar-C-N, C-12); 148.52 (-C=N-,C-13); 150.40 (-C=C-O, C-14); 194.38 (C=O, C-15).
Anal. Calcd. for C33H34N2O4: C, 75.83; H, 6.58; N, 5.36; O, 12.28; found: C, 75.84; H, 6.56;
N, 5.34; O, 12.24
9-(3-(3-methoxyphenyl)-1-phenyl-1H-pyrazol-4-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-
hexahydro-1H-xanthene-1,8(2H)-dione (3b)
Yield: 69%; pale yellow solid; m.p: 150–153 °C; IR (KBr, cm-1): 3052, 2855, 2882, 1719,
1628, 1593; 1H NMR (DMSO d6, 400 MHz) δ: 0.900 (s, 6H, CH3); 0.985 (s, 6H, CH3); 3.80(s,
3H, OCH3); 4.95 (s, 1H, C-H) 7.42 (s, 1H, Ar–H); 8.06 (s, 1H, CH); 13C NMR (DMSO d6,
400 MHz) δ: 28.61 (CH3, C-1); 32.04 (C(CH3)2, C-2); 117.63 (C-6); 129.39 (Ar–CH, C-10);
139.49 (Ar-C-N, C-12); 148.54 (-C=N-,C-13); 150.43 (-C=C-O, C-14); 194.42 (C=O, C-15).
Anal. Calcd. for C33H34N2O4: C, 75.85; H, 6.59; N, 5.36; O, 12.28; found: C, 75.84; H, 6.56;
N, 5.35; O, 12.20
9-(3-(4-bromophenyl)-1-phenyl-1H-pyrazol-4-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-
hexahydro-1H-xanthene-1,8(2H)-dione (3c)
Yield: 63%; yellow solid; m.p: 118–120 °C; IR (KBr, cm-1): 3050, 2921, 2885, 1721, 1622,
1595, 671; 1H NMR (DMSO d6, 400 MHz) δ: 0.904 (s, 6H, CH3); 0.993 (s, 6H, CH3); 2.29 (s,
4H, CH2); 7.62 (d, 2H, Ar–H); 8.08 (s, 1H, CH); 13C NMR (DMSO d6, 400 MHz) δ: 28.62
(CH3, C-1); 32.11 (C(CH3)2, C-2); 117.89 (C-6); 130.65 (Ar–CH, C-10); 139.38 (Ar-C-N, C-
12); 148.59 (-C=N-, C-13); 149.36(-C=C-O, C-14); 194.51 (C=O, C-15). Anal. Calcd. for
C32H31BrN2O3: C, 67.25; H, 5.47; N, 4.90; O, 8.41; found: C, 67.23; H, 5.41; N, 4.92; O, 8.38
9-(3-(4-chlorophenyl)-1-phenyl-1H-pyrazol-4-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-
hexahydro-1H-xanthene-1,8(2H)-dione (3d) Yield: 66%; white solid; m.p: 136–138 °C; IR (KBr, cm-1): 3062, 2918, 2875, 1718, 1624,
1592, 731; 1H NMR (DMSO d6, 400 MHz) δ: 0.906 (s, 6H, CH3); 0.995 (s, 6H, CH3); 2.32 (s,
4H, CH2); 7.67 (d, 2H, Ar–H); 8.15 (s, 1H, CH); 13C NMR (DMSO d6, 400 MHz) δ: 28.61
(CH3, C-1); 32.11 (C(CH3)2, C-2); 117.92 (C-6); 130.85 (Ar–CH, C-10); 139.28 (Ar-C-N, C-
12); 148.62 (-C=N-, C-13); 149.16(-C=C-O, C-14); 194.59 (C=O, C-15). Anal. Calcd. for
C32H31ClN2O3: C, 72.99; H, 5.95; N, 5.37; O, 9.41; found: C, 72.92; H, 5.85; N, 5.32; O, 9.11
3,3,6,6-tetramethyl-9-(1-phenyl-3-(p-tolyl)-1H-pyrazol-4-yl)-3,4,5,6,7,9-hexahydro-1H-
xanthene-1,8(2H)-dione (3e)
Yield: 79%; yellow solid; m.p: 133–135 °C; IR (KBr, cm-1): 3055, 2958, 2877, 1725, 1642,
1588; 1H NMR (DMSO d6, 400 MHz) δ: 0.902 (s, 6H, CH3); 0.985 (s, 6H, CH3); 2.88 (s, 3H,
CH3); 7.46 (s, 2H, Ar–H); 8.01 (s, 1H, CH); 13C NMR (DMSO d6, 400 MHz) δ: 28.62 (CH3,
C-1); 32.08 (C(CH3)2, C-2); 117.69 (C-6); 129.92 (Ar–CH, C-10); 139.62 (Ar-C-N, C-12);
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148.46 (-C=N-, C-13); 150.49 (-C=C-O, C-14); 194.28 (C=O, C-15). Anal. Calcd. for
C33H34N2O3: C, 78.32; H, 6.81; N, 5.59; O, 9.61; found: C, 78.23; H, 6.76; N, 5.53; O, 9.47
3,3,6,6-tetramethyl-9-(1-phenyl-3-(m-tolyl)-1H-pyrazol-4-yl)-3,4,5,6,7,9-hexahydro-1H-
xanthene-1,8(2H)-dione (3f)
Yield: 76%; yellow solid; m.p: 138-141 °C; IR (KBr, cm-1): 3055, 2955, 2876, 1725, 1624,
1585; 1H NMR (DMSO d6, 400 MHz) δ: 0.902 (s, 6H, CH3); 0.987 (s, 6H, CH3); 2.85 (s, 3H,
CH3); 7.42 (s, 2H, Ar–H); 8.03 (s, 1H, CH); 13C NMR (DMSO d6, 400 MHz) δ: 28.62 (CH3,
C-1); 32.09 (C(CH3)2, C-2); 117.65 (C-6); 129.98 (Ar–CH, C-10); 139.56 (Ar-C-N, C-12);
148.46 (-C=N-, C-13); 150.45 (-C=C-O, C-14); 194.28 (C=O, C-15). Anal. Calcd. for
C33H34N2O3: C, 78.32; H, 6.81; N, 5.59; O, 9.61; found: C, 78.23; H, 6.76; N, 5.53; O, 9.47
9-(3-(3-nitrophenyl)-1-phenyl-1H-pyrazol-4-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-
hexahydro-1H-xanthene-1,8(2H)-dione (3g)
Yield: 62%; yellow solid; m.p: 259–262 °C; IR (KBr, cm-1): 3070, 2956, 2874, 1698, 1622,
1590; 1H NMR (DMSO d6, 400 MHz) δ: 0.903 (s, 6H, CH3); 0.998 (s, 6H, CH3); 2.43 (s, 4H,
CH2); 7.77 (s, 2H, Ar–H); 8.10 (s, 1H, CH); 13C NMR (DMSO d6, 400 MHz) δ: 28.62 (CH3,
C-1); 32.12 (C(CH3)2, C-2); 117.55 (C-6); 130.40 (Ar–CH, C-10); 139.25 (Ar-C-N, C-12);
148.52 (-C=N-, C-13); 150.40 (-C=C-O, C-14); 194.38 (C=O, C-15). Anal. Calcd. for
C32H31N3O5: C, 71.49; H, 5.81; N, 7.82; O, 14.88; found: C, 71.47; H, 5.78; N, 7.85; O, 14.86
9-(3-(3-bromophenyl)-1-phenyl-1H-pyrazol-4-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-
hexahydro-1H-xanthene-1,8(2H)-dione (3h)
Yield: 51%; pale yellow solid; m.p: 125–127 °C; IR (KBr, cm-1): 3050, 2924, 2879, 1719,
1629, 1589, 677; 1H NMR (DMSO d6, 400 MHz) δ: 0.902 (s, 6H, CH3); 0.989 (s, 6H, CH3);
2.33 (s, 4H, CH2); 7.52 (d, 2H, Ar–H); 8.02 (s, 1H, CH); 13C NMR (DMSO d6, 400 MHz) δ:
28.62 (CH3, C-1); 32.08 (C(CH3)2, C-2); 117.69 (C-6); 130.85 (Ar–CH, C-10); 139.18 (Ar-C-
N, C-12); 148.75 (-C=N-, C-13); 149.42(-C=C-O, C-14); 194.51 (C=O, C-15). Anal. Calcd.
for C32H31BrN2O3: C, 67.25; H, 5.47; N, 4.90; O, 8.41; found: C, 67.19; H, 5.42; N, 4.92; O,
8.29
9-(3-(2-hydroxyphenyl)-1-phenyl-1H-pyrazol-4-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-
hexahydro-1H-xanthene-1,8(2H)-dione (3i)
Yield: 65%; white solid; m.p: 276-279 °C; IR (KBr, cm-1): 3064, 2944, 2876, 1712, 1680,
1568; 1H NMR (DMSO d6, 400 MHz) δ: 0.901 (s, 6H, CH3); 0.991 (s, 6H, CH3); 2.42 (s, 4H,
CH2); 7.52 (s, 2H, Ar–H); 8.09 (s, 1H, CH); 13C NMR (DMSO d6, 400 MHz) δ: 28.62 (CH3,
C-1); 32.10 (C(CH3)2, C-2); 117.52 (C-6); 130.22 (Ar–CH, C-10); 139.22 (Ar-C-N, C-12);
148.65 (-C=N-, C-13); 150.48 (-C=C-O, C-14); 194.34 (C=O, C-15). Anal. Calcd. for
C32H32N2O4: C, 75.59; H, 6.38; N, 5.51; O, 12.58; found: C, 75.57; H, 6.34; N, 5.45; O, 12.55
9-(3-(4-hydroxyphenyl)-1-phenyl-1H-pyrazol-4-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-
hexahydro-1H-xanthene-1,8(2H)-dione (3j)
Yield: 73%; white solid; m.p: 271-274 °C; IR (KBr, cm-1): 3068, 2940, 2880, 1715, 1674,
1566; 1H NMR (DMSO d6, 400 MHz) δ: 0.902 (s, 6H, CH3); 0.994 (s, 6H, CH3); 2.46 (s, 4H,
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CH2); 7.59 (s, 2H, Ar–H); 8.05 (s, 1H, CH); 13C NMR (DMSO d6, 400 MHz) δ: 28.62 (CH3,
C-1); 32.10 (C(CH3)2, C-2); 117.55 (C-6); 130.22 (Ar–CH, C-10); 139.30 (Ar-C-N, C-12);
148.70 (-C=N-, C-13); 150.45 (-C=C-O, C-14); 194.32 (C=O, C-15). Anal. Calcd. for
C32H32N2O4: C, 75.59; H, 6.38; N, 5.51; O, 12.58; found: C, 75.51; H, 6.32; N, 5.49; O, 12.56
3. 2. Biological evaluation
3. 2. 1. Antimicrobial activity
Antibacterial activity of synthesized derivatives was determined by using broth
microdilution method. Synthesized derivatives were tested against 4 isolated bacterial strains
Staphylococcus aureus, Streptococcus pyogenes, Escherichia coli and Pseudomonas
aeruginosa. Ampicillin, chloramphenicol and ciprofloxacin were used as standard drugs.
Compounds 3c, 3d, 3g and 3h displayed broad spectrum antibacterial activity against
both gram-positive and gram-negative bacteria as compared to standard drug ciprofloxacin.
Compounds 3c, 3d and 3h were found to be 4-fold (MIC = 12.5 µg/mL) more active against S.
aureus and 2-fold active (MIC = 25 µg/mL) against S. pyogens whereas compound 3g was
found to be 4-fold more potent against S. pyogens and 2-fold active against S. aureus compared
to the positive control ciprofloxacin. While compounds 3c, 3h showed equivalent activity
against E. coli and 3g, 3h showed equivalent potency against P. aeruginosa. High antibacterial
potency of 3c, 3d and 3h against gram-positive bacteria may be attributed to the presence of
electron withdrawing halogen substituents such as chloro and bromo present on phenyl ring of
pyrazolyl substitution.
In comparison to the standard drug griseofulvin, antifungal activity results indicated that
compound 3g substituted with nitro group at 3rd position of phenyl ring was found to be 2 fold
more potent against C. albicans and 4 fold more active against A. clavatus.
Table 2. In vitro antimicrobial activity of synthesized molecular scaffolds (3a-3j)
Code
Minimal inhibitory concentration (µg mL-1 )
(MIC)
S.a S. p E.c P.a C. a A. n A.c
3a 500 1000 500 100 1000 >1000 1000
3b 100 100 500 1000 >1000 500 1000
3c 12.5 25 25 50 500 500 250
3d 12.5 25 50 50 500 500 250
3e 100 100 250 125 500 500 1000
3f 500 1000 250 1000 500 500 >1000
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S.a = Staphylococcus aureus C.a = Candida albicans
S.p = Streptococcus pyogenes A.n = Aspergillus niger
E.c = Escherichia coli A.c = Aspergillus clavatus
P.a = Pseudomonas aeruginosa
3. 2. 2. Docking results
Docking studies revealed that among all docked compounds, compounds 3b, 3g and 3i
showed best binding conformation with the active site of receptor. It is clearly evident from
the values of MolDock score, Rerank score and HBond that these are the compounds having
least free energy at the binding site of PIM1 receptor.
Compounds 3b, 3g and 3i exhibited good Van der waals interaction and H-bond
formation with the amino acid residues present in the ATP binding pocket of PIM1 receptor.
Compound 3b is surrounded by amino acid residues Ala65, Arg122, Asn172, Asp128,
Asp131, Gln127, Glu171, Gly45, Ile185, Leu44, Leu174, Lys169, Phe49, Ser46, Val52 and
Val126 through Van der waals interaction. Compound 3b interacts with Asp128 through side
chain H-bond formation whereas steric interactions were observed with Asn172 and Leu174
by carbon atoms of phenyl side chain present on pyrazole ring.
Compound 3g is enclosed by amino acid residues Ala65, Arg122, Asn172, Asp128,
Asp131, Asp186, Gln127, Glu121 Glu171, Gly45, Ile104, Ile185, Leu43, Leu44, Leu120,
Leu174, Lys169, Phe49, Pro123, Val52 and Val126 through Van der waals interaction.
Compound 3g forms H-bond with Asp128 through N and O-atoms of nitro group present on
3rd position of phenyl substitution of pyrazole ring. Steric interactions were observed with
Asn172 and Leu174 by carbon atoms of phenyl side chain present on pyrazole ring, residues
Leu44 and Ala65 interact with methyl group of dimedone; carbonyl group of dimedone
interacts with Gly45 while Asp131 interacts through O-atom of nitro group.
3g 25 12.5 50 25 25 250 25
3h 12.5 25 25 25 500 250 250
3i 250 100 100 250 1000 500 250
3j 100 500 250 100 500 1000 >1000
Ampicillin 250 100 100 100 - - -
Chloramphenicol 50 50 50 50 - - -
Ciprofloxacin 50 50 25 25 - - -
Nystatin - - - - 250 100 100
Griseofulvin - - - - 50 100 100
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Compound 3i is bounded by amino acid residues Ala65, Arg122, Asn172, Asp128,
Asp131, Asp186, Gln127, Glu121 Glu171, Gly45, Ile104, Ile185, Leu43, Leu44, Leu174,
Phe49, Pro123, Val52 and Val126 through Van der waals interaction. Amino acid residues
Asp128 and Asp131 forms H-bond with compound 3i through O and H-atoms of -OH group
present on 2nd position of phenyl substitution of pyrazole ring. Steric interactions were
observed with Asn172, Leu174, Gln127, Val126 and Asp128 by carbon atoms of phenyl side
chain present on pyrazole ring, residues Leu44 and Ala65 interact with methyl group of
dimedone while carbonyl group of dimedone interacts with Gly45. The results reveal that
compounds 3b, 3g and 3i possess good binding affinity towards the ATP binding pocket of
Human PIM1 target receptor through Van der waals interaction, steric favorable interactions
and H-bond interactions.
Table 3. Docking score of compounds (3a-3j)
*Compounds are arranged based on their highest docking score
Compound MolDock Score* Rerank Score HBond
3g -144.899 -46.652 -2.258
3j -140.013 -19.532 0
3b -136.286 -82.969 -2.5
3d -135.838 -82.963 0
3c -135.561 -79.350 0
3h -130.953 -21.979 0
3i -129.840 -90.012 -2.328
3e -129.441 -74.153 0
3a -128.719 -69.848 0
3f -127.146 -81.446 -1.425
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..
Fig. 1. (a) ATP binding pocket of PIM1 receptor (1XQZ), (b), (c), (d) Amino acid residues
surrounding compounds 3b, 3g and 3i respectively, (e) H-bond formation between Asp 128 and
compound 3b shown by broken blue line, (f) Hydrogen donor (yellow shaded) and hydrogen
acceptor (blue shaded) favorable interactions of compound 3b
(a)
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Fig. 2. (g) H-bond formation between Asp 128 and compound 3g shown by broken blue line,
(h) steric interactions between amino acid residues of ATP binding pocket and compound 3g,
(i) Hydrogen donor (yellow shaded) and hydrogen acceptor (blue shaded) favorable interactions
(j)
(k)
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of compound 3g, (j) H-bond formation between amino acid residues (Asp 128, Asp 131) and
compound 3i shown by broken blue line, (k) steric interactions between amino acid residues of
ATP binding pocket and compound 3i, (l) Hydrogen donor (yellow shaded) and hydrogen
acceptor (blue shaded) favorable interactions of compound 3
4. CONCLUSIONS
In this present work, we have described the synthesis of a series of 9-(3-(aryl)-1-phenyl-
1H-pyrazol-4-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-hexahydro-1H-xanthene-1,8(2H)-dione
derivatives (3a-3j). The synthesized compounds were characterized by 1H NMR, 13C NMR and
IR spectroscopy and the obtained results are showing good agreement with the synthesized
structures. Amongst the synthesized compounds screened for their In vitro antimicrobial
activity, compounds 3c, 3d, 3g & 3h showed good potency as antibacterial agents and rest are
moderately active as compared to standard drug Ciprofloxacin while compound 3g exhibited
good antifungal activity against fungal species C.albicans and A.clavatus as compared to
standard drug Griseofulvin. Docking studies revealed that compounds 3b, 3g & 3i showed best
binding affinity towards the amino acid residues of ATP binding pocket of Human PIM1 target
receptor through Van der waals interaction, steric favorable interactions and H-bond
interaction. This provides future scope for their In vitro anti-cancer activity and establishes
them as better and newer drug candidates to produce future anticancer drugs by further
investigations.
Acknowledgement
Authors are thankful to Department of Chemistry, Kamani Science & Prataprai Arts College, Amreli for providing
laboratory facilities. The authors are also thankful to Department of Life Sciences, Gujarat University, Ahmedabad
for providing facilities for docking studies. Authors also express their gratitude towards NFDD (National Facility
for Drug Discovery), Saurashtra University, Rajkot for providing instrumentation support. Authors are also
thankful to Institute of Microbial Technology, Chandigarh, India for providing facility for antimicrobial activity.
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