Site-directed ligand discovery

We report a strategy (catled tethering) to discover low molecular weight ligands (approximate to 50 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 (approximate to 1,200 compounds) at concentrations typically used in drug screening (10 to 200 mu M). 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)approximate to 1 mM) was improved 3,000-fold by synthesis of a small set of analogs with the aid of crystallographic strucutres of the tethered complex. Such site-directed ligand discovery allows one to nucleate drug design from a spatially targeted lead fragment.