Investigating the Conformational Structure and Potential Site Interactions of SOD Inhibitors on Ec-SOD in Marine Mud Crab Scylla serrata: A Molecular Modeling Approach.
Superoxide dismutases (SODs) act as a first line of the enzymatic antioxidant defense system to control cellular superoxide anion toxicity. Previously, several inhibitors have been widely identified and catalogued for inhibition of SOD activity; however, still the information about the mechanism of interaction and points toward the inhibitor interactions in structures of SODs in general and in extracellular (Ec)-SOD in particular is still in naive. In the present research, we present an insight to elucidate the molecular basis of interactions of SOD inhibitors with Ec-SOD in mud crab Scylla serrata using molecular modeling and docking approaches. Different inhibitors of SOD such as hydrogen peroxide [Formula: see text], potassium cyanide, sodium dodecyl sulfate (SDS), [Formula: see text]-mercaptoethanol and dithiocarbamate were screened to understand the potential sites that may act as sites for cleavage or blocking in the protein. SOD-SDS and [Formula: see text] complex interactions indicate residues Pro72 and Asp102 of the predicted crab Ec-SOD as common targets. The GOLD result indicates that Pro72, Asp102 and Thr103 are commonly acting as the site of interaction in Ec-SOD of S. serrata with SOD inhibitors. For the first time, the results of this study provide an insight into the structural properties of Ec-SOD of S. serrata and define the possible involvements between the amino acids present in its active sites, i.e., in the regions from 70 to 84 and from 101 to 103 and different inhibitors.
Department of Zoology, College of Basic Science and Humanities, Orissa University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India. biswaranjanpaital@gmail.com.
Biswaranjan
B
Paital
Plant Functional Biology and Climate Change Cluster C3, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.
Gaurav
G
Sablok
Bioinformatics Centre, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India. skybiotech@gmail.com.|National Bureau of Agriculturally Important Microorganisms (NBAIM), Indian Council of Agricultural Research (ICAR), Govt. of India, Mau, Uttar Pradesh, 275103, India. skybiotech@gmail.com.
Sunil
S
Kumar
Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, 630003, India.
Sanjeev Kumar
SK
Singh
Department of Biotechnology, Utkal University, Bhubaneswar, India.
G B N
GB
Chainy
D000595:Amino Acid Sequence; D000818:Animals; D003386:Brachyura / Q000201:enzymology*; D020134:Catalytic Domain; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology*; D006861:Hydrogen Peroxide / Q000737:chemistry / Q000494:pharmacology; D008958:Models, Molecular; D011190:Potassium Cyanide / Q000737:chemistry / Q000494:pharmacology; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry / Q000494:pharmacology; D013482:Superoxide Dismutase / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism
D004791:Enzyme Inhibitors; D012967:Sodium Dodecyl Sulfate; D006861:Hydrogen Peroxide; D013482:Superoxide Dismutase; D011190:Potassium Cyanide
Enzyme inhibition mechanism; Extracellular superoxide dismutase; Molecular dynamics; Scylla serrata; Superoxide anion toxicity