title: Ligand supported homology modeling and docking evaluation of CCR2: docked pose selection by consensus scoring.
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.
authors.affiliation: Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea. jonghoon@yonsei.ac.kr
authors.forename: Jong-Hoon
authors.initials: JH
authors.lastname: Kim
authors.forename: Jee Woong
authors.initials: JW
authors.lastname: Lim
authors.forename: Seung-Woo
authors.initials: SW
authors.lastname: Lee
authors.forename: Kyoungrak
authors.initials: K
authors.lastname: Kim
authors.forename: Kyoung Tai
authors.initials: KT
authors.lastname: No
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D002461:Cell Line, Transformed; D016384:Consensus Sequence; D016208:Databases, Factual; D057809:HEK293 Cells; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D018343:Receptors, Adrenergic, beta-2 / Q000737:chemistry; D054390:Receptors, CCR2 / Q000037:antagonists & inhibitors / Q000737:chemistry*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D054852:Small Molecule Libraries / Q000737:chemistry; D040681:Structural Homology, Protein
chemical_list: D008024:Ligands; D018343:Receptors, Adrenergic, beta-2; D054390:Receptors, CCR2; D054852:Small Molecule Libraries