A mating mechanism to generate diversity for the Darwinian selection of DNA-encoded synthetic molecules

DNA-encoded library technologies empower the screening of synthetic molecules but have thus far not tapped into the power of Darwinian selection with iterative cycles of selection, amplification and diversification.  Herein we report a simple strategy to rapidly assemble libraries of conformationally constrained peptides that are paired in a combinatorial fashion (suprabodies).  We demonstrate that the pairing can be shuffled after each amplification cycle in a process akin to DNA shuffling or mating to regenerate diversity. Using simulations, we show the benefit of this recombination in yielding a more accurate correlation of selection fitness with affinity after multiple rounds of selection, particularly if the starting library is heterogeneous in the concentration of its members.  The method was validated with selections against streptavidin and applied to the discovery of PD-L1 binders.  We further demonstrate that the binding of self-assembled suprabodies can be recapitulated by smaller (ca. 7 KDa) synthetic products that maintain the conformational constrain of the peptides.  A selective suprabody binding PD-L1 with an affinity of 70nM was identified.