Protein structure similarity clustering and natural product structure as guiding principles for chemical genomics.
The majority of all proteins are modularly built from a limited set of approximately 1,000 structural domains. The knowledge of a common protein fold topology in the ligand-sensing cores of protein domains can be exploited for the design of small-molecule libraries in the development of inhibitors and ligands. Thus, a novel strategy of clustering protein domain cores based exclusively on structure similarity considerations (protein structure similarity clustering, PSSC) has been successfully applied to the development of small-molecule inhibitors of acetylcholinesterase and the 11beta-hydroxysteroid dehydrogenases based on the structure of a naturally occurring Cdc25 inhibitor. The efficiency of making use of the scaffolds of natural products as biologically prevalidated starting points for the design of compound libraries is further highlighted by the development of benzopyran-based FXR ligands.
Koch
M A
MA
Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Dortmund, Germany.
Waldmann
H
H
D042842:11-beta-Hydroxysteroid Dehydrogenases / Q000378:metabolism; D000818:Animals; D001665:Binding Sites; D002384:Catalysis; D002626:Chemistry, Pharmaceutical; D016000:Cluster Analysis; D006801:Humans; D008024:Ligands; D008956:Models, Chemical; D008968:Molecular Conformation; D010597:Pharmacogenetics / Q000379:methods*; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D018160:Receptors, Cytoplasmic and Nuclear / Q000378:metabolism; D012189:Retrospective Studies; D020687:cdc25 Phosphatases / Q000378:metabolism
D008024:Ligands; D011506:Proteins; D018160:Receptors, Cytoplasmic and Nuclear; D042842:11-beta-Hydroxysteroid Dehydrogenases; C517004:CDC25A protein, human; D020687:cdc25 Phosphatases