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OJBTM
Online Journal of Bioinformatics ©
Volume 18(2):47-52, 2017.
Docking
of alpha glucosidase with Pterocarpus santalinus linn (red
sandalwood) for management of diabetes
mellitus.
Chanra Sekhar Challa1., Saradamma Bulle2., Vaddi
Damodara Reddy3., Devanna
Nayakanti4., Varadacharyulu
Nallanchakravarthula5*
1Department of Chemistry, Jawaharlal Nehru Technological
University, Anantapur, 515 002 235Biochemistry,
Sri Krishnadevaraya University, Anantapur,
515 003, 4Chemistry, Jawaharlal Nehru Technological University, Anantapur, 515 002, Andhra Pradesh, India.
ABSTRACT
Challa CS1., Bulle S, Reddy VD., Nayakanti D, Nallanchakravarthula V., Docking alpha glucosidase with Pterocarpus santalinus linn (red
sandalwood) for management of diabetes mellitus, Onl
J Bioinform., 18(2):47-52,
2017. Inhibition
of Alpha-glucosidase (AG) has been recently recommended for management of
diabetes. Twenty bioactives in Pterocarpus santalinus Linn methanol extracts (PS) were identified by gas chromatography
(GC-MS). Anti-cataract activity on AG (PDB ID:2QLY)
was tested by docking with PS compounds. Unnecessary chains and hetero atoms
were removed from AG with SPDBV software and hydrogens added for identification
of active sites. CASTp was used to locate and measure
protein pockets and cavities and docking with GOLD sofware.
Parameters for AG were population size (100), selection pressure (1.1), number
of operations (10,000), number of island (1) and niche size (2). Crossover, mutation and migration parameters
were 100, 100 and 10 with cutoff values of 3.0 A° (dH-X) for hydrogen bonds and 6.0 A° for vanderwaals.
During docking, default algorithm speed and ligand binding site in targets were
defined within a 10 A° radius with the centroid as CE atom of active
residues. Number of poses for each
inhibitor was set at 100 and terminated if 3 ligand bound conformations were
within 1.5A° RMSD. After docking. each
binding pose was visualized for interaction with AG and most energetically
favorable conformation for Caffeine ligand, selected. Results revealed that of
20 compounds tested, CycloHexane, 1-ethyl-1-methyl,2,4-bis(1-methyl,ethanyl) showed highest docking energy
with AG.
Key words:
Anti-Diabetic, Docking studies, Alpha Glucosidase, Pterocarpus santalinus Linn