synthesis, characterization and docking studies of some ......synthesis, characterization and...

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: [email protected]

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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World Scientific News 118 (2019) 100-114

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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)


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)


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,






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)







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)


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,






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,



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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.

Referencs

[1] Xu C, Bartley JK, Enache DI, et al: High surface area MgO as a highly effective heterogeneous base catalyst for michael addition and knoevenagel condensation

reactions. Synthesis 2005: 3468–3476.

[2] Milan M, Viktor M, Rudolf K, Dusan I: Preparation of cyclic 1, 3-diketones and their exploitation in the synthesis of heterocycles. (2004) Curr Org Chem 8: 695–714.

[3] Hatakeyama S, Ochi N, Numata H, Takano S: A new route to substituted 3-methoxycarbonyldihydropyrans; enantioselective synthesis of (–)-methyl elenolate. J.

Chem. Soc., Chem. Commun. 17, 1988, 0, 1202-1204

[4] Song G, Wang B, Luo H, Yang L: Fe 3+-montmorillonite as a cost-effective and recyclable solid acidic catalyst for the synthesis of xanthenediones. (2007), Catal

Commun 8, 4, 673–676.


-113-

[5] Lynen F: Biosynthetic pathways from acetate to natural products. (1967), Pure Appl Chem 14: 137–168.

[6] Gérard EM, Sahin H, Encinas A, Bräse S: Systematic study of a solvent-free mechanochemically induced domino oxa-Michael-Aldol reaction in a ball mill. (2008),

Synlett 2008, 2702–2704.

[7] Chatterjee S, Iqbal M, Kauer JC, et al: Xanthene derived potent nonpeptidic inhibitors of recombinant human calpain I. (1996), Bioorg Med Chem Lett 6: 1619–1622.

[8] Nishiyama T, Sakita K, Fuchigami T, Fukui T: Antioxidant activities of fused heterocyclic compounds, xanthene-2, 7-diols with BHT or catechol skeleton. (1998)

Polym Degrad Stab 62: 529–534.

[9] Hafez H, Hegab M, Ahmed-Farag I, El-Gazzar A: A facile regioselective synthesis of novel spiro-thioxanthene and spiro-xanthene-9′,2-[1,3,4]thiadiazole derivatives as

potential analgesic and anti-inflammatory agents. (2008), Bioorg Med Chem Lett 18:

4538–4543.

[10] a) Menchen S. M. S. C, Benson J. Y. L, Lam W, Zhen D, Sun B. B, Rosenblum S. H, Khan U. S, Taing M: Chem. Abstr (2003), 139: 54287f.

b) Reynolds G. A, Tuccio S. A, Peterson, O. G: Chem. Abstr (1971), 71: 81334c.

[11] Hunter RC, Beveridge TJ: Application of a pH-sensitive fluoroprobe (C-SNARF-4) for pH microenvironment analysis in Pseudomonas aeruginosa biofilms. (2005); Appl

Environ Microbiol; 71: 2501–2510.

[12] Ahmad M, King TA, Ko D-K, et al: Performance and photostability of xanthene and pyrromethene laser dyes in sol-gel phases. J Phys Appl Phys (2002); 35:1473.

[13] Deutsch E, Maggiorella L, Eschwege P, et al: Environmental, genetic, and molecular features of prostate cancer. (2004), Lancet Oncol 5: 303–313.

[14] Nakhi A, Adepu R, Rambabu D, et al: Thieno [3, 2-c] pyran-4-one based novel small molecules: Their synthesis, crystal structure analysis and in vitro evaluation as potential

anticancer agents, (2012), Bioorg Med Chem Lett 22: 4418–4427.

[15] Winter JM, Brennan MF, Tang LH, et al: Survival after resection of pancreatic adenocarcinoma: results from a single institution over three decades. (2012), Ann Surg

Oncol 19: 169–175.

[16] Alvarez-Cubero MJ, Saiz M, Martinez-Gonzalez LJ, et al: Genetic analysis of the principal genes related to prostate cancer: a review. Urol Oncol. 2013 Nov; 31(8): 1419-

29.

[17] Siegel RL, Miller KD, Jemal A: Cancer statistics. (2016), CA Cancer J Clin 66:7–30.

[18] Tietze LF: Domino reactions in organic synthesis. (1996), Chem Rev 96: 115–136.

[19] Enders D, Grondal C, Huettl MR: Asymmetric organocatalytic domino reactions. (2007), Angew Chem Int Ed; 46: 1570–1581.

https://www.ncbi.nlm.nih.gov/pubmed/23141781


-114-

[20] Gewali MB, Tezuka Y, Banskota AH, et al: Epicalyxin F and Calyxin I: Two Novel Antiproliferative Diarylheptanoids from the Seeds of Alpinia b lepharocalyx. (1999),

Org Lett 1: 1733–1736.

[21] Merkel AL, Meggers E, Ocker M: PIM1 kinase as a target for cancer therapy. (2012), Expert Opin Investig Drugs 21: 425–436.

[22] Jin T-S, Zhang J-S, Wang A-Q, Li T-S: Ultrasound-assisted synthesis of 1, 8-dioxo-octahydroxanthene derivatives catalyzed by p-dodecylbenzenesulfonic acid in aqueous

media. (2006), Ultrason Sonochem 13: 220–224.

[23] Darviche F, Balalaie S, Chadegani F, Salehi P: Diammonium Hydrogen Phosphate as a Neutral and Efficient Catalyst for Synthesis of 1, 8‐Dioxo‐Octahydroxanthene

Derivatives in Aqueous Media. (2007), Synth Commun 37: 1059–1066.

[24] Shaterian HR, Hosseinian A, Ghashang M: Reaction in dry media: silica gel supported ferric chloride catalyzed synthesis of 1, 8-dioxo- octahydroxanthene derivatives. (2008),

Phosphorus Sulfur Silicon 183: 3136–3144.

[25] Shakibaei GI, Mirzaei P, Bazgir A: Dowex-50W promoted synthesis of 14-aryl-14H-dibenzo [a, j] xanthene and 1, 8-dioxo-octahydroxanthene derivatives under solvent-free

conditions. (2007), Appl Catal Gen 325: 188–192.

[26] Chavan AP: A Versatile and Practical Synthesis of 1, 8-Dioxo-octahydroxanthene Derivatives Catalyzed by Polyethylene Glycol (PEG) in Water. (2009), J Korean Chem

Soc 53: 415.

[27] Shetty, S.; Bhagat, V. Asian Journal of Chemistry (2008), 20, 5037.

[28] Isenberg, D. Biol (2001), 39, 221.

[29] Zgoda, J.; Porter, J. Pharmaceutical Biology (2001), 39, 221.

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