A simple method for determining compound affinity and chemical yield from DNA-encoded library selections

DNA-encoded libraries (DELs) can contain billions of unique chemical species; selecting against such large inputs, it is typical to find more candidate binders than is reasonable to pursue for follow-up synthesis and testing. Given this wealth of choices, common practice is to limit synthesis to only those compounds estimated to have the greatest chance of being high-affinity binders; of the many potential factors contributing to this estimation, the strength of the selection signal of a candidate binder is always important. We define here methods and equations which relate the theoretical selection signal of a compound to its affinity and chemical yield. Tests using known binders of BRD4 and ROCK2 support the theory backing these equations and suggest they should be of use for prospectively determining affinity and chemical yield from primary DEL selection data. •Method and equations to fit affinity and chemical yield of a DNA-tagged ligand binding to an immobilized protein.•Method uses physical conditions common to DEL selection, applicable to single ligands, or pools of ligands.•Experimental data supports these equations as sufficient to describe the binding physics of DEL selections, and supports the extension of these methods to other selection targets.