Patent ID: 7202033

Claim:
A method for identifying ligands binding to an inactive conformation of a target protein kinase, comprising (a) contacting the inactive conformation of said protein kinase having a first and a second binding site of interest and containing or modified to contain a nucleophile at or near the first site of interest with a plurality of ligand candidates, said candidates having a functional group reactive with the nucleophile, under conditions such that a reversible covalent bond is formed between the nucleophile and a candidate that has affinity for the first site of interest, to form a kinase-first ligand complex; (b) identifying the first ligand from the complex of (a); (c) designing a derivative of the first ligand identified in (a) to provide a small molecule extender (SME) having a first functional group reactive with the nucleophile on the kinase and a second functional group reactive with a second ligand having affinity for the second binding site of interest; (d) contacting the SME with the kinase to form a kinase-SME complex, and (e) contacting the kinase-SME complex with a plurality of second ligand candidates, said candidates having a functional group reactive with the SME in said kinase-SME complex, wherein a candidate that has affinity for said second binding site of interest on said kinase forms a reversible covalent bond with said kinase-SME complex, whereby a second ligand is identified.