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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.
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