Antibacterial Property and Molecular Docking Studies of Leaf Calli Phytochemicals of Bridelia scandens Wild.

Shivakumar, Venkatarangaiah, Shastri, Nagaraja, and Sheshagiri: Antibacterial Property and Molecular Docking Studies of Leaf Calli Phytochemicals of Bridelia scandens Wild.

Authors

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INTRODUCTION

Since earliest times, medicinal plants have been known to exert healing properties against human infections as antimicrobial agents due to the presence of rich secondary metabolites. Unscientific collection and over exploitation of medicinal plants resulted in the dwindling of natural population and many of them are at the verge of threatening status. Induction of callus from the medicinal plant parts and in vitro production of secondary metabolites from the calli is a novel technique for sustainable conservation of medicinal plants. So that callus culture is the process that can reduce the time and season as it does not need to have the whole plant cultivation and sacrificing it for extraction.1

Bridelia scandens is a straggling climber belongs to the family Euphorbiaceae. It is distributed in the warm regions of Southeast Asia2 and also in Western peninsular India especially in deciduous to semi-evergreen forests of Maharashtra, Kerala, Karnataka states (http://www.indiabiodiversity.org). In traditional medicine, decoction of the leaves has been used in the treatment of asthma, cough, fever, pleurisy, exudation and sores in mouth. The phytochemical examination of the B. scandens leaves showed the presence of flavonoids, carbohydrates, glycosides, phenolic compounds and tannins.3 In the previous study an anticancerous compound anthrisine-deoxypodophyllotoxin was isolated from the leaves of B. scandens.4

Over the past decade, much attention has been placed on the study of phytochemicals for their antibacterial activity, especially against multidrug-resistant Gram-negative and Gram-positive bacteria.5 The emergence of multidrug-resistance among bacteria has challenged the effectiveness of antibiotics in the advent of modern medicine and as such, antibiotic resistance has become one of the most serious health care problems in the world.6 Considering the above, there is a need to develop new effective antibacterial agents that circumvent the emergence of resistance. Nevertheless, the discovery of new antibiotics is very expensive and time consuming, requiring about ten years to bring a new antibiotic to market. Therefore, the search for antibacterial substances derived from natural products, such as phytochemicals, has gained cumulative importance.7

In addition, in silico prediction of the ADMET properties plays an important role in antibiotic drug discovery process. Nowadays ADME (absorption, distribution, metabolism and elimination) is applied at an early phase of the drug development process, in order to remove molecules with poor ADME properties from the drug development pipeline and leads to significant savings in research and development costs. Lipinski “Rule of five” is widely used as a filter for drug-like properties.8 Molecular docking is a frequently used method for evaluating the complex formation of small ligands with large biomolecules.9 In view of the above, the present investigation was undertaken to isolate and characterize antibacterial compounds from the in vitro derived leaf calli and to authenticate the antibacterial property against human pathogenic clinical isolates.

MATERIALS AND METHODS

Plant material and callus culture

Mesristematic leaf explants of B. scandens was collected from Bhadra Wild Life Sanctuary of the Western Ghats (1 km from Kuvempu University) and was identified by Prof. V Krishna, professor and taxonomist, Dept. of Biotechnology, Kuvempu University.

The leaves were cleaned with deionized water, sterilized with 5% tween-20, 0.2% mercuric chloride, followed by distilled water wash and then 1cm aseptically inoculated on to MS semi solid media supplemented with hormonal concentration of 0.5 mg/L BAP and 0.5 mg/L 2,4-D for callus initiation. The calli was subcultured on the same media and mass propagated for 4-6weeks. The calli was harvested, dried in hot air oven at 40ºC for 4 to 5 days.

Preparation of Extract

About 186 g of dried callus was subjected for cold extraction with methanol for about 48h. The extract was sieved (Whatman No.1 filter paper) and concentrated in vacuum under reduced pressure using rotary flash evaporator (Buchi, Flawil, Switzerland) and dried at desiccator.

Phytochemical screening

Determination of total phenol

Total phenol content in leaf callus methanol extract LCME was estimated by the Folin–Ciocalteu method.10 1 ml of LCME (50 μg) was mixed with Folin–Ciocalteu reagent (2 ml) (diluted 1:10, v/v) followed by the addition of 2 ml of sodium carbonate (7.5%, w/v) and mixed, allowed to reaction for 90 min at room temperature and absorbance was measured against the blank at 750 nm using spectrophotometer (Systronics, PC based double beam spectrophotometer 2202). Total phenol content of the extract was expressed in terms of equivalent to gallic acid (GAE, mg−1 of dry mass).

Determination of total flavonoid

Total flavonoid content of LCME was measured according to the modified method of Zhishen.11 5 ml of extract (200 μg) was mixed with 300 μl of 5% sodium nitrite and 300 μl of 10% aluminum chloride followed by the addition of 2 ml of 1 M sodium hydroxide after the incubation of reaction mixture at room temperature for 6 min. The volume in each test tube was made up to 10 ml by adding 2.4 ml of millipore water. Absorbance was measured at 510 nm against the blank. Total flavonoid content of the extract was expressed in terms of equivalent to catechin (mg−1 of dry mass).

Determination of alkaloid

Alkaloid determination using Harborne method:12 5 g of the sample was weighed into a 250 ml beaker and 200 ml of 10% acetic acid in ethanol was added and covered and allowed to stand for 4 h. This was filtered, and the extract was concentrated on a water bath to one-quarter of the original volume. Concentrated ammonium hydroxide was added drop wise to the extract until the precipitation was complete. The whole solution was allowed to settle and the precipitated was collected and washed with dilute ammonium hydroxide and then filtered. The residue is the alkaloid, which was dried and weighed.

HR-LCMS analysis of LCME

The bioactive components of B. scandens leaf callus extract was analyzed by High Resolution Liquid Chromatograph Mass Spectrometer (HR-LCMS) G6550A system (Agilent technologies). The method used for Chromatography was 30 mins ± ESI 10032014_MSMS.m. The Gas temperature used for analysis was 250°C. The theoretical mass of protonated compound was used for identification. HR-LC-MS analysis of B scandens bark extracts was performed at Sophisticated Analytical Instrument Facility (SAIF), Indian Institute of Technology, Mumbai, India. The compounds were identified by comparison with their retention time (RT) and mass with stored metlin library available with IIT, Bombay.

Antibacterial activity

Microbial strains

The antibacterial activity of the LCME was individually tested against a set of five bacterial human pathogenic clinical isolates obtained from Shivamogga Institute of Medical Sciences, Shivamogga, Karnataka, namely: Staphylococcus aureus, Streptococcus pneumoniae. Pseudomonas aeruginosa, Salmonella typhi, and Vibrio cholera, Bacterial isolates were cultured overnight at 37°C in nutrient agar (NA) media.

Disk diffusion assay

Determination of antibacterial activity of LCME was evaluated by agar well diffusion method. The extract was dissolved in DMSO at different concentrations (500, 1000 and 1500 μg/m1 of DMSO μg). 100 μl of the suspension containing 108 colony forming units CFU/ml of bacteria were spread on NA media, respectively. Wells were made on agar plates using sterile cork borer, and 20 μl of LCME of each concentration were introduced into appropriately marked wells, ciprofloxacin (20 μg/ml) was taken as a positive control. Then culture plates incubated for 24 h at 37°C. Antibacterial activity was assessed by measuring the diameter of the growth inhibition zone in millimeters for the test organisms compared to the control. Activity index was calculated for comparison of the zone of inhibition of test material with standard antibiotic using the formula AI (Activity Index) = ZI of Test/ZI of Standard.13

Minimum Inhibitory Concentration (MIC)

The MIC of the LCME was evaluated by modified resazurin (7-Hydroxy-3H-phenoxazin-3-one 10-oxide) microtitre plate assay.14 50 μl of test sample containing 250 μg of extract [5 mg/ml (w/v)] solutions in 10% dimethyl sulfoxide (DMSO, v/v) and 50 μg of standard antibiotic [1 mg/ml (w/v)] solutions in 10% DMSO. 50 μl of nutrient broth was added to all wells (microtitre plate). Two-fold serial dilutions were performed using a pipette such that each well had 50 μl of the test material in serially descending concentrations. 30 μl of 3.3 times stronger hi sensitivity broth and 10 μl of resazurin indicator solution (prepared by dissolving 27 mg resazurin in 4 ml of sterile distilled water) were added to each well. Finally, 10 μl of bacterial suspension was added to the appropriate wells to achieve a concentration of approx 5×106 CFU/ml. The analysis of variance (ANOVA) was performed using ezANOVA (version 0.98) software and Microsoft excel to determine the mean and standard error.

Molecular docking studies

Lipinski “Rule of five” is commonly used as a filter for drug-like properties.8 The in silico pharmacokinetic properties and ADME (absorption, distribution, metabolism and elimination) and toxicity analysis were predicted using Data Warrior (http://www.openmolecules.org/datawarrior.html). Data Warrior tries to assess the toxicity risk by finding substructures within the chemical structure being indicative of a toxicity risk within one of said four major toxicity classes.

The chemical structure of HR-LCMS identified compounds namely, azaperone, bifonazole, fusidic acid, lasalocid and quinine and the standard drug ciprofloxcin were drawn using Chem Bio Draw tool (Chem Bio Office Ultra 14.0 suite) assigned with proper 2D orientation, and structure of each was checked for structural drawing error. Energy of each molecule was minimized using ChemBio3D. The energy minimized ligand molecules were then used as input for AutoDock Vina, in order to carry out the docking simulation. The protein data bank (PDB) coordinate file with the name ‘2XCT.pdb’ was used as receptor molecule.15 All the water molecules were removed from the receptor. The graphical user interface program MGL tool was used to set the grid box for docking simulations. The grid was set so that it surrounds the region of interest in the macromolecule. The grid box volume was set to 8, 14, and 14 Å for x, y, and z dimensions, respectively, and the grid center was set to 3.194, 43.143, and 69.977 for x, y, and z center, respectively, which covered all the ten amino acid residues in the considered active pocket. The docking algorithm provided with AutoDock Vina was used to search for the best docked conformation between ligand and protein. During the docking process, a maximum of ten conformers were considered for each ligand. Molecular docking was performed in Corei5 Intel processor CPU with 6 GB DDR3 RAM. AutoDock Vina16 was compiled and run in a Windows 8.0 professional operating system. LigPlot+17 and PyMol educational version were used to deduce the 2D and 3D pictorial representation of the interaction between the ligands and the receptor. The ligands are represented in green colour, H-bonds with their respective distances are represented with cyan colour, and the interacting residues are represented in ball and stick model representation.

RESULTS

Callus culture

Leaf explants of B scandens proliferated into callus mass on MS media fortified with 0.5 mg/l BAP and 0.5 mg/l 2, 4-D. Callus induction was noticed from the cut end of the lamina and dorsal vein of the explants (Figure 1). Subculturing of the calli on to the same media induced luxuriant proliferation of the fleshy callus mass. After 6 weeks, the callus mass was harvested and fresh weight was found to be 3000 g the calli mass was dried in oven at 40°C for 4 days and dry weight was found to be 200 g of the dried calli mass was extracted with methanol used for phytochemical and antibacterial screening.

Figure 1

Callus induction from the leaf segments of Bridelia scandens A- Bridelia scandens collected from Bhadra Wild Life Sanctuary of Western Ghats, India. B-Callus induction from the excised lamina of B. scandens on MS media with 0.5 mg/L BAP and 0.5 mg/L 2, 4-D. C-Mass production of callus. D-Dried leaf calli mass of B. scandens.

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Phytochemical analysis

The preliminary phytochemical analysis of LCME showed positive result for qualitative tests for the phytochemicals alkaloids, flavonoids, and phenolics (Table 1). In quantitative analysis total polyphenolic content in LCME was expressed as equivalent to gallic acid (GAE) and is found to be 37.2 μg/mg of dry extract. The flavonoid concentration of LCME was expressed as equivalent to catechin and is found to be 56.9 μg/mg of dry extract. The alkaloid concentration of LCME was found to be 63.4 μg/mg of dry extract as depicted in the Table 1.

Table 1

Qualitative and Quantitative analysis of B. scandens LCME.

Qualitative testConcentration μg/gm
Alkaloids+63.4 μg/gm
Flavonoids+56.9 μg/gm
Steroids--
Terpenoids--
Cardiac glycosides--
Saponins--
Tannins--
Phenols+37.2 μg/gm

MCE – Methanol Callus extract, +: Present and -: Absent.

HR-LCMS analysis

HR-LCMS analysis of LCME resulted the presence of 100 phytoconstituents (Table 2) and the chromatogram of the phytoconstituents is shown in Figure 2. Among them the compounds azaperone, bifonazole, fusidic acid, lasalocid and quinine were known for antibacterial properties.

Table 2

Phytoconstituents of leaf calli Methanol extract obtained from HR-LCMS.

Compound LabelRTMassFormulaDB Diff (ppm)Hits
Cpd 1: Trolamine2.27149.1039C6 H15 N O38.741
Cpd 2: Diaminopimelic acid4.767190.0929C7 H14 N2 O412.9715
Cpd 3: Trolamine4.82149.104C6 H15 N O37.851
Cpd 4: METARAMINOL4.82167.0937C9 H13 N O25.4314
Cpd 5: Trp Tyr7.109367.1537C20 H21 N3 O4-1.315
Cpd 6: Trp Tyr7.268367.1537C20 H21 N3 O4-1.4215
Cpd 7: 1,2-Benzenediol, 4- [[4-(4-fluorophenyl)-3-piperidinyl] methoxy]-, (3S- trans)7.269317.1424C18 H20 F N O30.915
Cpd 8: Ser Leu Met7.269349.1683C14 H27 N3 O5 S-3.2515
Cpd 9: Asn Cys Ser7.271322.0974C10 H18 N4 O6 S-8.319
Cpd 10: 17-phenyl-trinor- PGF2alpha7.59388.2207C23 H32 O510.891
Cpd 11: 18-acetoxy- PGF2alpha-11-acetate7.854454.2561C24 H38 O81.37
Cpd 12: His Ile Trp7.854454.227C23 H30 N6 O412.9215
Cpd 13: N-(4- benzenesulfonamide) arachidonoyl amine8.081458.2605C26 H38 N2 O3 S-0.314
Cpd 14: 26,26,26,27,27,27- hexafluoro-1alpha,25- dihydroxyvitamin D3 /26,26,26,27,27,27-hexafluoro1alpha,25-8.278524.2677C27 H38 F6 O39.263
Cpd 15: Tolbutamide8.605270.1058C12 H18 N2 O3 S-7.2610
Cpd 16: Hydroxylysine10.089162.1008C6 H14 N2 O3-2.285
Cpd 17: sebacic acid10.089202.1161C10 H18 O421.624
Cpd 18: Zolazepam10.277286.1242C15 H15 F N4 O-4.415
Cpd 19: Val Asn Gly10.445288.143C11 H20 N4 O51.412
Cpd 20: 8- cyclopentyltheophyllin10.448248.125C12 H16 N4 O29.39
Cpd 21: Tolbutamide10.451270.1037C12 H18 N2 O3 S0.4111
Cpd 22: Met Asn Gly12.312320.1119C11 H20 N4 O5 S11.1614
Cpd 23: 6-Ketoestriol12.312302.1524C18 H22 O4-2.0415
Cpd 24: Laminaribiose12.313342.1198C12 H22 O11-10.5415
Cpd 25: 12.812.8331.13281.2315
Cpd 26: Hydroxythiopental13.006258.1066C11 H18 N2 O3 S-10.795
Cpd 27: Asn Asn Gly13.077303.116C10 H17 N5 O66.356
Cpd 28: Methylergonovine13.094339.1978C20 H25 N3 O2-9.1415
Cpd 29: Esmolol13.364295.1777C16 H25 N O42.1715
Cpd 30: 13.60713.607186.1163
Cpd 31: Methylergonovine13.703339.1976C20 H25 N3 O2-8.515
Cpd 32: Asp Val Glu13.703361.1529C14 H23 N3 O8-12.0515
Cpd 33: EVOXINE13.802347.1403C18 H21 N O6-9.9615
Cpd 34: Leu Ser Glu13.804347.17C14 H25 N3 O7-2.0815
Cpd 35: azaperone13.988327.1735C19 H22 F N3 O3.5715
Cpd 36: Glu Ala Ile14.786331.1721C14 H25 N3 O66.7115
Cpd 37: Cuscohygrine14.884224.1873C13 H24 N2 O6.822
Cpd 38: Anandamide 0- phosphate14.986427.2497C22 H38 N O5 P-2.1215
Cpd 39: (E)-2- Methylglutaconic acid15.639144.0434C6 H8 O4-7.868
Cpd 40: Arg Arg Glu16.304459.2509C17 H33 N9 O69.7713
Cpd 41: 2-[3-Carboxy-3- (methylammonio)propyl]-L- histidine16.537270.1321C11 H18 N4 O42.444
Cpd 42: DEOXYGEDUNOL ACETATE16.893510.2715C30 H38 O7-192
Cpd 43: 16.89316.893537.3174
Cpd 44: GPCho(9:0/9:0)16.894538.357C26 H53 N O8 P-11.3511
Cpd 45: GPGro(18:1(9E)/0:0) [U]16.894510.3029C24 H47 O9 P-13.983
Cpd 46: Enkephaline, (D- Ala)2-Leu17.972569.2743C29 H39 N5 O718.735
Cpd 47: Maltotriitol17.973506.1786C18 H34 O1611.972
Cpd 48: 13-Hydroxypergolide glucuronide17.978506.2118C25 H34 N2 O7 S-6.153
Cpd 49: 3- Hydroxydodecanedioic acid18.248246.1438C12 H22 O511.83
Cpd 50: Isosorbide-2- glucuronide18.561322.0913C12 H18 O10-4.29
Cpd 51: Doxapram18.782378.2307C24 H30 N2 O20.0715
Cpd 52: BIFONAZOLE19.072310.1477C22 H18 N2-2.294
Cpd 53: 4-Amino-6,7- dimethoxy-2-(1- piperazinyl) quinazoline19.346289.1545C14 H19 N5 O2-2.287
Cpd 54: Met Tyr19.347312.1146C14 H20 N2 O4 S-0.765
Cpd 55: 3,5,3’,5’-Tetra-tert- butyldiphenoquinone19.752408.3045C28 H40 O2-4.143
Cpd 56: 3beta,6alpha,7alpha- Trihydroxy-5beta-cholan-24-oic Acid19.758408.2823C24 H40 O512.9615
Cpd 57: 19.86019.86792.5443
Cpd 58: GPIns(16:0/16:0)19.861810.5154C41 H79 O13 P12.921
Cpd 59: GPA (18:0/22:6(4Z,7Z,10Z,1319.973748.4841C43 H73 O8 P26.941
Cpd 60: 19.97519.975770.4228
Cpd 61: Di- demethylcitalopram20.067296.1309C18 H17 F N2 O5.223
Cpd 62: GPGro(16:0/16:0) [U]20.081722.5023C38 H75 O10 P10.33
Cpd 63: 20.08220.082704.4151
Cpd 64: GPEtn(18:0/18:1(11Z))20.085717.5187C39 H76 N O8 P16.8913
Cpd 65: 20.08720.087704.4538
Cpd 66: 20.20320.203682.4211
Cpd 67: 20.20620.206677.453
Cpd 68: 20.20620.206660.3938
Cpd 69: 20.22420.224660.4271
Cpd 70: Digitoxigenin bisdigitoxoside20.322634.3769C35 H54 O10-8.221
Cpd 71: 20.32220.322616.438
Cpd 72: PHORBOL MYRISTATE ACETATE20.325616.4027C36 H56 O8-8.363
Cpd 73: C16 Sphinganine20.378273.2637C16 H35 N O211.381
Cpd 74: Coenzyme Q620.446590.421C39 H58 O421.181
Cpd 75: LASALOCID20.447590.3863C34 H54 O8-7.522
Cpd 76: 16-Glutaryloxy-1alpha,25-dihydroxyvitamin D320.563546.3598C32 H50 O7-7.662
Cpd 77: (Z)-2-hexacos-17- enamidoethanesulfonic acid20.879501.3738C28 H55 N O4 S22.761
Cpd 78: 20.91820.918147.9941
Cpd 79: O- Desmethylquinidine20.938310.1695C19 H22 N2 O2-4.415
Cpd 80: 21.06021.06315.273
Cpd 81: GPGro(14:0/14:0) [U]21.231666.4367C34 H67 O10 P15.694
Cpd 82: 1,25- ihydroxyvitamin D3 3-21.486578.3861C33 H54 O8-7.323
Cpd 83: Fusidic acid21.629516.3489C31 H48 O6-7.362
Cpd 84: Quinine21.691324.1852C20 H24 N2 O2-4.4715
Cpd 85: 1alpha,25-dihydroxy 2alpha-(3- hydroxypropoxy) vitamin D321.754490.3671C30 H50 O5-2.5914
Cpd 86: 25-hydroxy-1beta- hydroxymethyl-26,27- dimethyl-24a-homo-22,23,24,24a-tetradehydro 3- epivitamin D3 / 221.759468.3547C31 H48 O311.9615
Cpd 87: 26,27-dinor- 3alpha,6alpha,12alpha- trihydroxy-5beta-cholestan-24-one21.891406.318C25 H42 O4-23.815
Cpd 88: 1alpha,25-dihydroxy 26,27-dimethyl-20,21- didehydro-23-oxavitamin D3 / 1alpha,25-dihydroxy-26,27- dime21.891446.3393C28 H46 O40.7815
Cpd 89: C17 Sphinganine-1- phosphate21.975384.279C17 H41 N2 O5 P-9.622
Cpd 90: 11beta-PGF2alpha- d422.094358.2641C20 H30 D4 O54.4215
Cpd 91: Anandamide (18:3, n-6)22.169321.2707C20 H35 N O2-12.1812
Cpd 92: 22.63722.637438.3662
Cpd 93: 27-nor-5b- cholestane-3a,7a,12a,24,25- pentol22.638438.3382C26 H46 O5-8.286
Cpd 94: Gln Ile Thr23.45360.1987C15 H28 N4 O66.0815
Cpd 95: Nuatigenin24.891430.315C27 H42 O4-15.6615
Cpd 96: Testosterone isocaproate25.059386.292C25 H38 O3-25.631
Cpd 97: 27.40227.402337.3252
Cpd 98: 27.51527.515352.9191
Cpd 99: Procainamide27.586235.1663C13 H21 N3 O9.41
Cpd 100: 27.59427.594524.5037
Figure 2

HR-LCMS Chromatograph of B. scandens leaf calli methanol extract

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Antibacterial activity

The antibacterial activity of LCME was evaluated at the concentrations of 500, 1000 and 1500 μg/m1 of DMSO. 1500 μg/m1 concentration shows significant antibacterial property noticed against clinical pathogen strains Staphylococcus aureus (17.67±0.88 mm.d.), Streptococcus pneumonia (13.67±0.33), Pseudomonas aeruginosa (16.33±0.67), Salmonella typhi (17.67±0.33), and Vibrio cholera (15.33±0.33), as compared to the standard drug ciprofloxacin. The MIC assay was performed by modified resazurin assay the extract shows highest inhibitory activity against S.aureus with a significant MIC value of 1.10±0.15×10-2. Inhibition of bacterial strains are summarized in Table 3.

Table 3

Zone of inhibition and MIC values of LCME against pathogenic bacterial strains.

SL. NoInhibition zone diameter (mm) and MIC (mg/ml-1)
MicroorganismZI of LCME (1500 μg/well)Activity indexMICZI of Ciprofloxacin (20 μg/well)MIC
1S.aureus17.67±0.880.6971.10±0.15×10-225.33±0.673.16±0.10×10-3
2S.pneumoniae13.67±0.330.4947.12±0.01×10-227.67±0.333.16±0.10×10-3
3V.cholerae15.33±0.330.6053.10±0.15×10-225.33±0.885.82±0.10×10-3
4P.aeruginosa16.33±0.670.6206.30±0.10×10-226.33±0.330.60±0.30×10-3
5S.typhi17.67±0.330.7571.20±0.01×10-224.33±0.331.56±0.10×10-3

Values are mean±standard error (n=3) of three different samples, analyzed individually in triplicate, ZI, the diameter of inhibition zone (mm) including well diameter of 6 mm, MIC, minimum inhibitory concentration (mg/ml). AI (Activity Index) = ZI of Test/ZI of Standard.

Toxicity prediction

Result of pharmacokinetic properties and toxicity analysis of 5 compounds (azaperone, bifonazole, fusidic acid, lasalocid and quinine) identified by HR-LCMS is shown in Table 4. All the 5 compounds obey the Lipinski’s ‘Rule of 5 limit better LogS values and were free from mutagenic tumorigenic, reproductive and irritant effect. In general, a poor solubility is associated with bad absorption and the aqueous solubility (Log S) of the compound which significantly affects its absorption and distribution characteristics. Based on the results from the DataWarrior, LogP, better LogS, good drug score and less toxicity risk parameters are predicted as shown in the Table 4.

Table 4

In silico ADMET and drug likeness prediction using data warrior.

CompoundscLogPCLogSH-AcceptorsH-DONORSTPSADrug likeness
Azaperone2.76-3.424036.445.409
Bifonazole4.757-6.8442017.822.0429
Fusidic acid5.823-5.36363104.060.050
Lasalocid5.363-6.11884133.522.5589
Quinine2.61-3.094145.590.878

Molecular Docking

In association with in vitro antimicrobial activity, it is useful to carry out in silico studies to predict the orientation and binding affinity at the active site of the receptor. The molecular docking of HR-LCMS identified ligand molecules- azaperone, bifonazole, fusidic acid, lasalocid and quinine with bacterial enzyme DNA gyrase is shown in Figure 3. Among them the compound lasalocid exhibited better docking efficiency with DNA gyrase. It forms two hydrogen bonds with amino acids Arg1122, and Gly1082 in the active site of the target protein with bond length 2.86 and 3.09 respectively, with the least binding affinity -4.9 and hence is considered as the best dock conformation (Table 5). Compound azaperone forms two hydrogen bonds with Gly1082 and Ser1085 amino acids with bond length 3.11 and 2.98 Å. The compound bifonazole forms only one hydrogen bond with the amino acid Ser108 with bond length 3.18 Å and the compound Fusidic acid forms two hydrogen bonding with Asp437 and Ser1085 with bond length 2.89 and 2.91 Å respectively. While compound quinine doesn’t form hydrogen bond with the aminoacids of the active pocket. However, all these docked molecules exhibited more hydrophobic interaction than the standard drug ciprofloxacin. The RMSD has often been used to measure the quality of reproduction of a known binding pose by molecules with ligands. All docked molecules have zero RMSD values as shown in the Table 5.

Figure 3

2D and 3D protein-ligand interaction DNA gyrase with the ligands azaperone bifonazole, fusidic acid and lasalocid.

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Table 5

Molecular docking values of LCME compounds obtained from LCMS analysis.

LIGANDAFFINITY (kcal/mol)H-BONDSH-BOND LENGTH (ź)H-BOND WITHHYDROPHOBIC INTERACTIONS
azaperone-4.422.982XCT:Ser1085::AZA:OABGly436, Asp437, Gly459, His1081, Arg1122, Phe1123
3.112XCT:Gly1082::AZA:OAB
bifonazole-4.313.182XCT:Ser1084::BIF:NABArg458, Gly459, Gly1082,Arg1122, Phe1123
fusidic acid-4.722.892XCT:Asp437::FUS:OACArg458,Gly459, Lys460, His1081, Gly1082, Ser1084, Arg1122,Phe1123,
2.912XCT:Ser1085::FUS:OAF
lasalocid-4.922.862XCT:Arg1122::LAS:OACGly436, Asp437, Gly459, Asp512, Ser1084, Ser1085, Phe1123,
3.092XCT:Gly1082::LAS:OAE
quinine-4.6---Cys300, Gly301, Leu484, Glu488, Leu601, Ala602, Lys603, Ser604, Val605
ciprofloxacin-4.412XCT:Arg1122::CIP:OAQAsp512, Ser1084, Ser1085

DISCUSSION

Medicinal plants have been used as a source of medicine in all cultures since times immemorial.18 Even though World Health Organization reported that the primary health care system for the 60% population of the world is represented by the traditional medicines yet a great number of plant species with potential biological activities were unexplored.19 The extracts of several medicinal plants are very effective against microbial as well as parasitic infections.20 Although synthetic or chemical drugs as compared to herbal medicines can have greater or quicker effects, but they possess many adverse effects and risks.21 Herbal medicines are generally less expensive as compared to synthetic ones.

The continuous exploitation of several medicinal plant species from the wild.22 and substantial loss of their habitats during past 15 years have resulted in population decline of many high value medicinal plant species over the years. The primary threats to medicinal plants are those that affect any kind of biodiversity used by humans.23,24 Attempts are being made by different organizations to cultivate various medicinal plant species, including rare and endangered categories.25 Evidence that plant cell cultures are able to produce secondary metabolites came quite late in the history of in vitro techniques.26

Callus culture is very useful to obtain commercially important secondary metabolites or drugs can be directly extracted from the callus tissues without scarifying the whole plant. In the present study, HR-LCMS analysis of LCME showed the presence of various compounds. Among them the compounds azaperone, bifonazole, fusidic acid, lasalocid and quinine are reported as good antibacterial agents27-30 As compared to in vivo plant parts the de novo synthesis of secondary metabolites takes place in the in vitro derived calli due to the influence of hormones supplemented in the media. The standardized technique can be explored commercially for the mass production of compounds.

S. aureus bacteremia is a significant cause of morbidity and mortality in neutropenic patients with cancer.31 In the present study LCME of B. scandens exhibited significant inhibitory effect on both gram positive Staphylococcus aureus, Streptococcus pneumoniae. Pseudomonas aeruginosa and gram negative Salmonella typhi, Vibrio cholera, strains which causes pneumonia (lung infection), osteomyelitis (bone infection), endocarditis (heart infection), phlebitis (infection of veins and blood vessels), mastitis (infection of breast and formation of abscesses) and meningitis (brain infections).in humans. Previous investigator Adeeba Anjum.32 evaluated the antibacterial property of B. scandens leaf and stem bark against 13 bacterial clinical isolates both gram positive (Bacillius cereus, Bacillus megaterium, Bacillus subtilis, Sarcina lutea, Staphylococcus aereus) and gram negative (Escherichia coli, Pseudomonas aeruginosa, Salmonella paratyphi, Salmonella typhi, Shigella boydii, Shigella dysenteriae, Vibro meniscus, Vibrio parahaemolyticus) The methanol extract of the leaf exhibited the highest activity against S. lutea of 21.6mm and for S. aereus 19.1mm ZI. LCME shows 17.6mm ZI. The antibacterial property of LCME is due the cumulative effect of the compounds azaperone, bifonazole, fusidic acid, lasalocid and quinine and it was supported by molecular docking studies. The in silico docking of lasalocid with the DNA gyrase showed higher binding affinity as well as hydrogen bonding and good hydrophobic interaction with the receptor. Among these 5 ligands lasalocid showed highest binding affinity and hydrophobic interaction with the amino acids of the active pocket. DNA gyrase is an essential bacterial enzyme that catalyzes the introduction of negative (−) supercoils into chromosomal and plasmid DNA. Gyrase was discovered soon after it was clear that in vitro recombination of bacteriophage λ required a negatively supercoiled DNA substrate. DNA gyrase cleave and religate DNA to regulate DNA topology and are a major class of antibacterial and anticancer drug targets.33 The 5 ligand molecules exhibited the antibacterial activity by hindering the function of DNA gyrase.

CONCLUSION

Leaf calli methanol extract of B. scandens contains good antibacterial compounds azaperone, bifonazole, fusidic acid, lasalocid and quinine. The antibacterial activity was more significant against S. aureus. In silico docking studies also supported the inhibition of DNA gyras with highest bonding efficiency and hydropobic interaction. Due to unscientific over exploitation many of the medicinal are becoming endangered. The harvesting of antibacterial compunds from the in vitro grown leaf calli of Bridelia scandens is a better method to combat contagious microbial diseases.

ACKNOWLEDGEMENT

The authors are thankful to DBT, New Delhi, India for providing financial support through DBT- BUILDER program (Order No. BT/PR9128/INF/22/190/2013, Dated: 30/06/2015) and the Kuvempu University administrative authority for offering the facility to carry out the work.

CONFLICT OF INTEREST

No Conflict of Interest.

ABBREVIATIONS

LCME

Leaf callus methanol Extract

BAP

6-Benzylaminopurine

2.4-D

2,4-Dichlorophenoxyacetic acid

MS

Murashige and Skoog

DMSO

Dimethyl sulfoxide

RMSD

Root Mean Square Deviation

ZI

Zone of Inhibition

MIC

Minimum Inhibitory Concentration

HR-LCMS-

High Resolution Liquid Chromatograph Mass Spectrometer

ADMET

Absorption, Distribution, Metabolism, Excretion and Toxicity.

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GRAPHICAL ABSTRACT

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SUMMARY

  • Evaluation of antibacterial activity and molecular docking studies of B. scandens leaf Calli extract was performed.

  • LCME show significant antibacterial activity against selected human clinical pathogens.

  • And the molecular docking shows phyto components obtained from the LCME shows good inhibition against bacterial DNA gyrase.

  • The present study shows that the LCME is a good antibacterial agent against human clinical pathogen.

ABOUT AUTHORS

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Mr.Ravikumar S, Research Scholar, Department of Biotechnology, Kuvempu University. He is having two years of research experience.

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Dr. V Krishna, Professor, Department of PG studies and research in Biotechnology, Kuvempu University. He is having 27 years of teaching and research experience in the field of Plant tissue culture, Phytochemistry and Pharmacology. He is currently running 5 crore project and has received research grants from various funding agencies like DBT, DST, UGC etc. He has published 185 research papers in international and national peer reviewed journals. He is having one patent to his credit.

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Mr. Sudhesh Shastri, Research Scholar, Department of Biotechnology, Kuvempu University. He is having three years of research experience. He has published two research articles in peer reviewed journals.

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Mr. Ravishankara B, Research Scholar, Department of Biotechnology, Kuvempu University. He is having two years of research experience.

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Mr. Ajith S, Research Scholar, Department of Biotechnology, Kuvempu University. He is having two years of research experience.