74
D. Lahiri et al.
structure of intimin has been used as a template to model the structure of biofilmforming protein using SWISS-MODEL online server. PHYRE2 online server has
been used to model protein structure using fold recognition. The best models were
further used in the docking study.
2.13 Protein-Ligand Docking Using Schrodinger
2.13.1 Ligand Docking
The docking calculations were performed with Schrödinger 2015 suite of softwares.
All non-bonded heteroatoms and water molecules were removed and hydrogen bonds
were added to optimize the structure. The biofilm protein grid file and quercetin were
docked using Glide standard precision. This docked structure was again used as the
receptor grid file and allicin was docked to understand the synergistic mechanism of
binding. Glide score was used to infer the affinity and binding energy values (Guex
and Peitsch 1997).
2.14 Statistical Analysis
All the data were of sample size 5 and were represented as Mean ± SE.
3 Results and Discussion
3.1 Biochemical Estimation of Plant Compounds
3.1.1 Total Phenolic (TPC) and Flavonoid Content (TFC)
The total flavonoids and polyphenol content of A. cepa extract were determined
using quercetin and gallic acid as standard samples by colorimetric assays (Fig. 1a).
The high flavonoid content (6.54 ± 0.02 µg/ml) and total polyphenol content
(102.819±0.05 µg/ml) of A. cepa indicated the antioxidant potential of the plant
extract (Fig. 1).
3.1.2 Hydrogen Peroxide and Hydroxyl Radical Scavenging Activity
Hydrogen peroxide activity and IC 50 value of the extract of A. cepa compared to the
control Ascorbic acid revealed the fact that the efficacy of the plant extract was better
D. Lahiri et al.
structure of intimin has been used as a template to model the structure of biofilmforming protein using SWISS-MODEL online server. PHYRE2 online server has
been used to model protein structure using fold recognition. The best models were
further used in the docking study.
2.13 Protein-Ligand Docking Using Schrodinger
2.13.1 Ligand Docking
The docking calculations were performed with Schrödinger 2015 suite of softwares.
All non-bonded heteroatoms and water molecules were removed and hydrogen bonds
were added to optimize the structure. The biofilm protein grid file and quercetin were
docked using Glide standard precision. This docked structure was again used as the
receptor grid file and allicin was docked to understand the synergistic mechanism of
binding. Glide score was used to infer the affinity and binding energy values (Guex
and Peitsch 1997).
2.14 Statistical Analysis
All the data were of sample size 5 and were represented as Mean ± SE.
3 Results and Discussion
3.1 Biochemical Estimation of Plant Compounds
3.1.1 Total Phenolic (TPC) and Flavonoid Content (TFC)
The total flavonoids and polyphenol content of A. cepa extract were determined
using quercetin and gallic acid as standard samples by colorimetric assays (Fig. 1a).
The high flavonoid content (6.54 ± 0.02 µg/ml) and total polyphenol content
(102.819±0.05 µg/ml) of A. cepa indicated the antioxidant potential of the plant
extract (Fig. 1).
3.1.2 Hydrogen Peroxide and Hydroxyl Radical Scavenging Activity
Hydrogen peroxide activity and IC 50 value of the extract of A. cepa compared to the
control Ascorbic acid revealed the fact that the efficacy of the plant extract was better