title: Site-directed ligand discovery.
abstract: We report a strategy (called "tethering") to discover low molecular weight ligands ( approximately 250 Da) that bind weakly to targeted sites on proteins through an intermediary disulfide tether. A native or engineered cysteine in a protein is allowed to react reversibly with a small library of disulfide-containing molecules ( approximately 1,200 compounds) at concentrations typically used in drug screening (10 to 200 microM). The cysteine-captured ligands, which are readily identified by MS, are among the most stable complexes, even though in the absence of the covalent tether the ligands may bind very weakly. This method was applied to generate a potent inhibitor for thymidylate synthase, an essential enzyme in pyrimidine metabolism with therapeutic applications in cancer and infectious diseases. The affinity of the untethered ligand (K(i) approximately 1 mM) was improved 3,000-fold by synthesis of a small set of analogs with the aid of crystallographic structures of the tethered complex. Such site-directed ligand discovery allows one to nucleate drug design from a spatially targeted lead fragment.
authors.affiliation: Sunesis Pharmaceuticals, Incorporated, Redwood City, CA 94063, USA. erlanson@sunesis-pharma.com
authors.forename: D A
authors.initials: DA
authors.lastname: Erlanson
authors.forename: A C
authors.initials: AC
authors.lastname: Braisted
authors.forename: D R
authors.initials: DR
authors.lastname: Raphael
authors.forename: M
authors.initials: M
authors.lastname: Randal
authors.forename: R M
authors.initials: RM
authors.lastname: Stroud
authors.forename: E M
authors.initials: EM
authors.lastname: Gordon
authors.forename: J A
authors.initials: JA
authors.lastname: Wells
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D001665:Binding Sites; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000235:genetics / Q000378:metabolism; D004220:Disulfides / Q000378:metabolism; D015195:Drug Design; D004926:Escherichia coli / Q000201:enzymology; D018698:Glutamic Acid / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D008970:Molecular Weight; D019151:Peptide Library; D011392:Proline / Q000031:analogs & derivatives / Q000378:metabolism; D011487:Protein Conformation; D015202:Protein Engineering; D013816:Thermodynamics; D013940:Thymidylate Synthase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D004220:Disulfides; D008024:Ligands; D019151:Peptide Library; D018698:Glutamic Acid; D011392:Proline; D013940:Thymidylate Synthase; D003545:Cysteine