Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Molecular Docking Study of Aminoacyl-tRNA Synthetases with Ligand Molecules from Four Different Scaffolds

  • Bharatham, Nagakumar (Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University) ;
  • Bharatham, Kavitha (Biomolecular Modeling and Design Division, Bioinformatics Institute) ;
  • Lee, Yu-No (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU)) ;
  • Kim, Song-Mi (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU)) ;
  • Lazar, Prettina (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU)) ;
  • Baek, A-Young (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU)) ;
  • Park, Chan-In (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU)) ;
  • Eum, Hee-Sung (Department of Chemistry and Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies) ;
  • Ha, Hyun-Joon (Department of Chemistry and Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies) ;
  • Yun, Sae-Young (Department of Chemistry, Sogang University) ;
  • Lee, Won-Koo (Department of Chemistry, Sogang University) ;
  • Kim, Sung-Hoon (Center for Medicinal Protein Network and Systems Biology, College of Pharmacy, Seoul National University) ;
  • Lee, Keun-Woo (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU))
  • Published : 2010.03.20
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Abstract

Aminoacyl-tRNA synthetases (aaRSs) play vital roles in protein biosynthesis of living organisms and are interesting antibacterial drug targets. In order to find out new inhibitor candidate molecules as antibacterial agent, the binding modes of the candidate molecules were investigated at the active sites of aaRSs by molecular docking study. The docking simulations were performed with 48 compounds from four different scaffolds into the eight different aaRSs. The results show that scaffolds 3 and 4 compounds have consistently better binding capabilities, specifically for HisRS (E. coli) and IleRS (S. aureus). The binding modes of the best compounds with the proteins were well compatible with those of two ligands in crystal structures. Therefore, we expect that the final compounds we present may have reasonable aaRS inhibitory activity.

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