Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.
Nat Chem. 2022 Feb;14(2):141-152. doi: 10.1038/s41557-021-00829-5. Epub 2021 Dec 6.
DNA-encoded library technologies enable 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. Here 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 similar to DNA shuffling or mating to regenerate diversity. Using simulations, we show the benefits 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 (∼7 kDa) synthetic products that maintain the conformational constraint of the peptides.
DNA 编码文库技术可用于筛选合成分子，但迄今为止尚未利用达尔文选择的力量进行迭代选择、扩增和多样化。在这里，我们报告了一种简单的策略，可以快速组装构象受限肽的文库，这些肽以组合方式配对（超体）。我们证明，在每个扩增循环之后，可以类似于 DNA 改组或交配的过程进行配对洗牌，以再生多样性。通过模拟，我们表明，这种重组在经过多轮选择后，更准确地将选择适应性与亲和力相关联，尤其是在起始文库中成员的浓度存在异质性的情况下。该方法通过针对链霉亲和素的选择进行了验证，并应用于 PD-L1 结合物的发现。我们进一步证明，通过保持肽构象约束的较小（约 7 kDa）合成产物可以再现自组装超体的结合。
