title: A structure-based strategy for discovery of small ligands binding to functionally unknown proteins: combination of in silico screening and surface plasmon resonance measurements.
abstract: In the postgenomic era, many researchers and organizations have been engaged in structural and functional analyses of proteins. As a part of these efforts, searching for small organic compounds that bind specifically to target proteins is quite important. In this study, we have developed a rational strategy for ligand discovery based on the three-dimensional structures of target proteins, which were elucidated by X-ray crystallography and nuclear magnetic resonance spectroscopy. The strategy has three features: (i) rapid selection of candidate compounds by in silico screening, (ii) automated preparation of sample solutions with robotics, and (iii) reliable evaluation of the candidates with surface plasmon resonance. Applying the strategy to a protein, At2g24940 from Arabidopsis thaliana, we discovered four small ligands out of a commercially available library of about 150 000 compounds. Although these compounds had only weak affinities to the target protein, with dissociation constants ranging from 68 to 120 microM, they apparently possess common structural features. They would be leads for the development of specific inhibitors/drugs for At2g24940, and provide important clues toward elucidation of the protein function.
authors.affiliation: Protein Research Group, RIKEN Genomic Sciences Center, Yokohama, Japan.
authors.forename: Naoei
authors.initials: N
authors.lastname: Yoshitani
authors.forename: Kazuhito
authors.initials: K
authors.lastname: Satou
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
authors.forename: Sakura
authors.initials: S
authors.lastname: Suzuki
authors.forename: Hideki
authors.initials: H
authors.lastname: Hatanaka
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Hirota
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D029681:Arabidopsis Proteins / Q000737:chemistry; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D015195:Drug Design; D008024:Ligands; D008958:Models, Molecular; D015394:Molecular Structure; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D020349:Surface Plasmon Resonance
chemical_list: D029681:Arabidopsis Proteins; D008024:Ligands; D011506:Proteins