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Journal of Molecular Modeling

, Volume 17, Issue 10, pp 2707–2716 | Cite as

Ligand supported homology modeling and docking evaluation of CCR2: docked pose selection by consensus scoring

  • Jong-Hoon Kim
  • Jee Woong Lim
  • Seung-Woo Lee
  • Kyoungrak Kim
  • Kyoung Tai No
Short Comment

Abstract

Chemokine receptor 2 (CCR2) is a G-protein coupled receptor (GPCR) and a crucial target for various inflammatory and autoimmune diseases. The structure based antagonists design for many GPCRs, including CCR2, is restricted by the lack of an experimental three dimensional structure. Homology modeling is widely used for the study of GPCR-ligand binding. Since there is substantial diversity for the ligand binding pocket and binding modes among GPCRs, the receptor-ligand binding mode predictions should be derived from homology modeling with supported ligand information. Thus, we modeled the binding of our proprietary CCR2 antagonist using ligand supported homology modeling followed by consensus scoring the docking evaluation based on all modeled binding sites. The protein-ligand model was then validated by visual inspection of receptor-ligand interaction for consistency of published site-directed mutagenesis data and virtual screening a decoy compound database. This model was able to successfully identify active compounds within the decoy database. Finally, additional hit compounds were identified through a docking-based virtual screening of a commercial database, followed by a biological assay to validate CCR2 inhibitory activity. Thus, this procedure can be employed to screen a large database of compounds to identify new CCR2 antagonists.

Keywords

CCR2 Consensus scoring Docking evaluation GPCR Ligand supported homology modeling Virtual screening 

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Jong-Hoon Kim
    • 1
    • 2
  • Jee Woong Lim
    • 2
    • 3
  • Seung-Woo Lee
    • 2
  • Kyoungrak Kim
    • 2
  • Kyoung Tai No
    • 1
    • 4
  1. 1.Department of BiotechnologyYonsei UniversitySeoulRepublic of Korea
  2. 2.Research and Development CenterYangJi ChemicalsSuwonRepublic of Korea
  3. 3.Department of ChemistrySejong UniversitySeoulRepublic of Korea
  4. 4.Bioinformatics and Molecular Design Research CenterSeoulRepublic of Korea

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