title: Improvement of Ligand Affinity and Thermodynamic Properties by NMR-Based Evaluation of Local Dynamics and Surface Complementarity in the Receptor-Bound State.
abstract: The thermodynamic properties of a ligand in the bound state affect its binding specificity. Strict binding specificity can be achieved by introducing multiple spatially defined interactions, such as hydrogen bonds and van der Waals interactions, into the ligand-receptor interface. These introduced interactions are characterized by restricted local dynamics and improved surface complementarity in the bound state. In this study, we experimentally evaluated the local dynamics and the surface complementarity of weak-affinity ligands in the receptor-bound state by forbidden coherence transfer analysis in free-bound exchange systems (Ex-FCT), using the interaction between a ligand, a myocyte-enhancer factor 2A (MEF2A) docking peptide, and a receptor, p38α, as a model system. The Ex-FCT analyses successfully provided information for the rational design of a ligand with higher affinity and preferable thermodynamic properties for p38α.
authors.affiliation: Biomedicinal Information Research Center (BIRC) and Molecular Profiling Research Center (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.|Japan Biological Informatics Consortium (JBIC), 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
authors.forename: Yumiko
authors.initials: Y
authors.lastname: Mizukoshi
authors.affiliation: Biomedicinal Information Research Center (BIRC) and Molecular Profiling Research Center (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
authors.forename: Koh
authors.initials: K
authors.lastname: Takeuchi
authors.affiliation: Biomedicinal Information Research Center (BIRC) and Molecular Profiling Research Center (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.|Japan Biological Informatics Consortium (JBIC), 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
authors.forename: Misa
authors.initials: M
authors.lastname: Arutaki
authors.affiliation: Biomedicinal Information Research Center (BIRC) and Molecular Profiling Research Center (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.|Japan Biological Informatics Consortium (JBIC), 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Tokunaga
authors.affiliation: Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Co. LTD., 1-16-13 Kitakasai, Edogawa-ku, Tokyo, 134-8630, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Takizawa
authors.affiliation: Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Co. LTD., 1-16-13 Kitakasai, Edogawa-ku, Tokyo, 134-8630, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Hanzawa
authors.affiliation: Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.|Biomedicinal Information Research Center (BIRC) and Molecular Profiling Research Center (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
authors.forename: Ichio
authors.initials: I
authors.lastname: Shimada
mesh_terms: D006801:Humans; D008024:Ligands; D064326:MEF2 Transcription Factors / Q000737:chemistry / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D013499:Surface Properties; D013816:Thermodynamics; D048051:p38 Mitogen-Activated Protein Kinases / Q000737:chemistry / Q000378:metabolism*
chemical_list: D008024:Ligands; D064326:MEF2 Transcription Factors; C578035:MEF2A protein, human; D048051:p38 Mitogen-Activated Protein Kinases
keywords: NMR spectroscopy; drug design; ligand-receptor interface; structural biology; surface complementarity