Molecular modeling and docking studies of glutamate racemase in Vibrio vulnificus CMCP6.
Identification of novel drug targets in silico in Vibrio vulnificus is important as it is one of the emerging pathogenic microorganisms. Glutamate racemase, an important constituent of bacterial cell wall is chosen for structure prediction using homology modeling. With the aid of tools and software like MODELLER and Swiss-PdbViewer, the 3D structure is predicted and the final model is refined by energy minimization. The quality of the refined model is assessed using PROCHECK. The interaction between the predicted structure of glutamate racemase and its potential inhibitors namely L-serine O-sulfate, (2R,4R)-2-amino-4-(2-benzo[b]thienyl)methyl pentanedioic acid, aziridino glutamate, exiguaquinol, gamma-2 naphthylmethyl-D-glutamate and D-glutamine is analysed in silico by Autodock. The results indicate that certain residues like Aspl3, Tyr45, Gly46, Asn78, Thr79, Cys185, His187 are highly conserved across the active site stretches of different bacterial species and may possibly assume precedence over the other residues for inhibitory action. This study provides an insight into the structure of glutamate racemase in V. vulnificus and also gives an idea about potential sites responsible for inhibitory action that could further be substantiated by experimental investigations.
Vidya
Natarajan
N
Department of Bioinformatics, HelixlnfoSystems, 132A, II Floor, Sterling Towers, IV Cross Street, Sterling Road, Chennai-600034, India.
Vadivukkarasi
Bagavathkumar
B
Manivannan
Gopalakrishnan
G
Anbarasu
Krishnan
K
D000591:Amino Acid Isomerases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D000595:Amino Acid Sequence; D020134:Catalytic Domain; D003198:Computer Simulation; D017124:Conserved Sequence; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D006860:Hydrogen Bonding; D021621:Imaging, Three-Dimensional; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D041261:Vibrio vulnificus / Q000201:enzymology*
D004791:Enzyme Inhibitors; D000591:Amino Acid Isomerases; C062292:glutamate racemase