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A method for the rapid and efficient identification of ligands to biological targets is reported. The combinatorial method does not require structural or mechanistic information and is accomplished in four straightforward steps. (i ) A set of potential binding elements is prepared wherein each molecule incorporates a common chemical linkage group. (ii ) The set of potential binding elements is screened to identify all binding elements that interact even weakly with the biological target. (iii ) A combinatorial library of linked binding elements is prepared whereby the binding elements are connected by the common chemical linkage groups through a set of flexible linkers. (iv ) The combinatorial library is screened to identify the tightest-binding ligands. The utility of the method was demonstrated by the identification of a potent and subtype-selective small molecule inhibitor of the non-receptor tyrosine kinase c-Src (IC50 = 64 nM). Because the method relies on connecting two distinct binding elements, the relative contributions of the two binding elements to the potency and selectivity of the inhibitor were readily determined. This information provides valuable insight into the molecular basis of inhibition.

Combinatorial target-guided ligand assembly: Identification of potent subtype-selective c-Src inhibitors