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 combinatorial library which is a ligand for a first biomolecule, wherein the mass-coded combinatorial library is of the general formula XYn, n is an integer from 2 to about 6, X is a scaffold and each Y is, independently, a peripheral moiety, the method comprising the steps:

• (a) producing the mass-coded combinatorial library, comprising
• (i) choosing every set of two different peripheral moiety precursors from a peripheral moiety precursor set, said choosing performed in a manner such that for each set of two, if the two peripheral moiety precursors have equal molecular masses, then one of the two is removed, forming a remaining set;
• (ii) from the remaining set, choosing every set of four peripheral moiety precursors, including for a given set of four, removing one of the four peripheral moiety precursors if a sum of the molecular masses of a first two precursors in the given set of four equals a sum of the molecular masses of a second two precursors in the given set of four peripheral moiety precursors, said choosing forming a remainder set;
• (iii) from the remainder set, choosing every set of six different peripheral moiety precursors, including for a given set of six, removing one of the six peripheral moiety precursors if a sum of the molecular masses of a first three precursors in the given set of six equals a sum of the molecular masses of a second three precursors in the given set of six, said choosing forming a working selection set;
• and
• (iv) from the working selection set of peripheral moiety precursors, choosing said peripheral moiety precursor subset such that said subset comprises a sufficient number of peripheral moiety precursors that there exist at least about 250 distinct combinations of n peripheral moieties derived from said subset, wherein each of at least about 90% of the combinations of n peripheral moieties derived from said subset have molecular mass sums that are distinct from the molecular mass sum of all other combinations of n peripheral moieties derived from said subset;
• and
• (v) contacting said peripheral moiety precursor subset with a scaffold precursor, said scaffold precursor having n reactive groups, wherein each reactive group is capable of reacting with at least one peripheral moiety precursor to form a covalent bond, under conditions sufficient for the reaction of each reactive group with a peripheral moiety precursor, thereby producing the mass-coded combinatorial library;
• (b) contacting the first biomolecule with the mass-coded combinatorial library, whereby members of the mass-coded combinatorial library which are ligands for the 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;
• (c) separating the first biomolecule-ligand complexes from the unbound members of the mass-coded combinatorial library;
• (d) dissociating the first biomolecule-ligand complexes;
• and
• (e) determining the molecular mass of each ligand to identify the set of n peripheral moieties present in each ligand;
• wherein the molecular mass of each ligand corresponds to a group of n peripheral moieties present in that ligand, thereby identifying a member of the mass-coded combinatorial library, which is a ligand for the first biomolecule.