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OJBTM
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
ABSTRACT
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.