Method for producing and screening mass-coded combinatorial libraries for drug discovery and target validation

A method for identifying a member of a mass-coded molecular library which is a ligand for a first biomolecule but is not a ligand for a second biomolecule, said method comprising the steps of:

• (a) contacting the second biomolecule with a mass-coded molecular library, said mass-coded molecular library comprising compounds of the general formula XYn, wherein n is an integer from 2 to about 6, X is a scaffold and each Y is, independently, a peripheral moiety, wherein there exist at least about 250 distinct combinations of n peripheral moieties, and wherein each of at least about 90% of the combinations of n peripheral moieties has a molecular mass sum that is distinct from the molecular mass sum of all other combinations of n peripheral moieties, whereby members of the mass-coded molecular library which are ligands for the second biomolecule bind to the second biomolecule to form second biomolecule-ligand complexes and members of the mass-coded library which are not ligands for the second biomolecule remain unbound;
• (b) separating the second biomolecule-ligand complexes from the unbound members of the mass-coded molecular library;
• (c) contacting the first biomolecule with the unbound members of the mass-coded molecular library of step (b), whereby members of the mass-coded molecular library which are ligands for the first biomolecule bind to the first biomolecule to form first biomolecule-ligand complexes and members of the mass-coded library which are not ligands for the first biomolecule remain unbound;
• (d) dissociating the first biomolecule-ligand complexes;
• and
• (e) determining the molecular mass of each ligand for the first biomolecule;
• wherein each molecular mass determined in step (e) corresponds to a set of n peripheral moieties present in a ligand for the first biomolecule which is not a ligand for the second biomolecule, thereby identifying a member of the mass-coded combinatorial library which is a ligand for the first biomolecule but is not a ligand for the second biomolecule.