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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.
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