Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Ligand Based Pharmacophore Identification and Molecular Docking Studies for Grb2 Inhibitors

  • Arulalapperumal, Venkatesh (Department of Biochemistry and Division of Applied Life Science (BK21), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of National Science (RINS), Gyeongsang National University (GNU)) ;
  • Sakkiah, Sugunadevi (Department of Biochemistry and Division of Applied Life Science (BK21), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of National Science (RINS), Gyeongsang National University (GNU)) ;
  • Thangapandian, Sundarapandian (Department of Biochemistry and Division of Applied Life Science (BK21), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of National Science (RINS), Gyeongsang National University (GNU)) ;
  • Lee, Yun-O (Department of Biochemistry and Division of Applied Life Science (BK21), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of National Science (RINS), Gyeongsang National University (GNU)) ;
  • Meganathan, Chandrasekaran (Department of Biochemistry and Division of Applied Life Science (BK21), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of National Science (RINS), Gyeongsang National University (GNU)) ;
  • Hwang, Swan (Department of Biochemistry and Division of Applied Life Science (BK21), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of National Science (RINS), Gyeongsang National University (GNU)) ;
  • Lee, Keun-Woo (Department of Biochemistry and Division of Applied Life Science (BK21), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of National Science (RINS), Gyeongsang National University (GNU))
  • Received : 2011.10.19
  • Accepted : 2012.02.23
  • Published : 2012.05.20
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Abstract

Grb2 is an adapter protein involved in the signal transduction and cell communication. The Grb2 is responsible for initiation of kinase signaling by Ras activation which leads to the modification in transcription. Ligand based pharmacophore approach was applied to built the suitable pharmacophore model for Grb2. The best pharmacophore model was selected based on the statistical values and then validated by Fischer's randomization method and test set. Hypo1 was selected as a best pharmacophore model based on its statistical values like high cost difference (182.22), lowest RMSD (1.273), and total cost (80.68). It contains four chemical features, one hydrogen bond acceptor (HBA), two hydrophobic (HY), and one ring aromatic (RA). Fischer's randomization results also shows that Hypo1 have a 95% significant level. The correlation coefficient of test set was 0.97 which was close to the training set value (0.94). Thus Hypo1 was used for virtual screening to find the potent inhibitors from various chemical databases. The screened compounds were filtered by Lipinski's rule of five, ADMET and subjected to molecular docking studies. Totally, 11 compounds were selected as a best potent leads from docking studies based on the consensus scoring function and critical interactions with the amino acids in Grb2 active site.

Keywords

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