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Online Journal of Bioinformatics ©
Volume 17(1):29-40, 2016
In silico agonist for human extracellular superoxide dismutase SOD3
Kanipakam Hema, Sandeep Swargam, Natarajan Pradeep and Amineni Umamaheswari,
SVIMS Bioinformatics Centre, SVIMS University, Tirupati– India
Hema K, Swargam S, Pradeep N, Umamaheswari A., In silico agonist for human extracellular superoxide dismutase SOD3, Onl J Bioinform., 17(1):29-40, 2016. We describe in silico agonists of human SOD3 with predicted active site residues. Structural analysis of human SOD3 retrieved from protein data bank was followed by high-throughput virtual screening. Multi-level molecular docking studies and Prime/MM–GBSA was used to calculate binding free energy (ΔG). Residues Arg-185, Asn-180, Asn-115, His-113 of human SOD3-lead 1 docking complex formed four hydrogen bonds and Arg-186 showed one π-cation interaction with lead 1. Residues His-113, His-124, Asn-180 and Arg-186 formed in the human SOD3 lead 1 docking complex. Lead 1 had binding affinity XP GScore -7.557 kcal/mol and free binding energy ΔG score -34.20 kcal/mol with binding orientation to human SOD3 greater than existing activators. Activation of SOD3 with lead 1 may reduce oxidative stress and endothelial damage.
Key words: Cardiovascular diseases, SOD3, Lead 1, Docking scores, Prime/MM–GBSA.