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

Research output: Contribution to journalArticle

16 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)2707-2716
Number of pages10
JournalJournal of Molecular Modeling
Volume17
Issue number10
DOIs
Publication statusPublished - 2011 Oct 1

Fingerprint

scoring
Chemokine Receptors
homology
Ligands
ligands
evaluation
decoys
G-Protein-Coupled Receptors
Proteins
Screening
proteins
Mutagenesis
screening
Binding sites
mutagenesis
Assays
Inspection
Binding Sites
inspection

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Computational Theory and Mathematics
  • Inorganic Chemistry

Cite this

Kim, Jong Hoon ; Lim, Jee Woong ; Lee, Seung Woo ; Kim, Kyoungrak ; No, Kyoung Tai. / Ligand supported homology modeling and docking evaluation of CCR2 : Docked pose selection by consensus scoring. In: Journal of Molecular Modeling. 2011 ; Vol. 17, No. 10. pp. 2707-2716.
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Ligand supported homology modeling and docking evaluation of CCR2 : Docked pose selection by consensus scoring. / Kim, Jong Hoon; Lim, Jee Woong; Lee, Seung Woo; Kim, Kyoungrak; No, Kyoung Tai.

In: Journal of Molecular Modeling, Vol. 17, No. 10, 01.10.2011, p. 2707-2716.

Research output: Contribution to journalArticle

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