Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Binding Mode Prediction of 5-Hydroxytryptamine 2C Receptor Ligands by Homology Modeling and Molecular Docking Analysis

  • Ahmed, Asif (Neuro-medicine centre, Life Sciences Division, Korea Institute of Science and Technology) ;
  • Nagarajan, Shanthi (Neuro-medicine centre, Life Sciences Division, Korea Institute of Science and Technology) ;
  • Doddareddy, Munikumar Reddy (Neuro-medicine centre, Life Sciences Division, Korea Institute of Science and Technology) ;
  • Cho, Yong-Seo (Neuro-medicine centre, Life Sciences Division, Korea Institute of Science and Technology) ;
  • Pae, Ae-Nim (Neuro-medicine centre, Life Sciences Division, Korea Institute of Science and Technology)
  • Received : 2011.02.08
  • Accepted : 2011.04.04
  • Published : 2011.06.20
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Abstract

Serotonin or 5-hydroxytryptamine subtype 2C ($5-HT_{2C}$) receptor belongs to class A amine subfamily of G-protein-coupled receptor (GPCR) super family and its ligands has therapeutic promise as anti-depressant and -obesity agents. So far, bovine rhodopsin from class A opsin subfamily was the mostly used X-ray crystal template to model this receptor. Here, we explained homology model using beta 2 adrenergic receptor (${\beta}$2AR), the model was energetically minimized and validated by flexible ligand docking with known agonists and antagonists. In the active site Asp134, Ser138 of transmembrane 3 (TM3), Arg195 of extracellular loop 2 (ECL2) and Tyr358 of TM7 were found as important residues to interact with agonists. In addition to these, V208 of ECL2 and N351 of TM7 was found to interact with antagonists. Several conserved residues including Trp324, Phe327 and Phe328 were also found to contribute hydrophobic interaction. The predicted ligand binding mode is in good agreement with published mutagenesis and homology model data. This new template derived homology model can be useful for further virtual screening based lead identification.

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