The Impact of Variable Selection Coverage on Detection of Ligands from a DNA-Encoded Library Screen

Selecting Approaches for Hit Identification and Increasing Options by Building the Efficient Discovery of Actionable Chemical Matter from DNA-Encoded Libraries

“…Taken together, these data strongly support this model and indicate that the magnitude of DEL signal has dependence on the overall operation of the experiment. There has been considerable focus in the field on normalizing DEL signals to enable their comparison, and while useful for within-sample comparisons of N-synthon pharmacophores, 76–78 our observation indicates that any calculations of enrichment that involve a normalization to the total population size of a sample will thus transfer the variability from this background into the hit compound signals. Without a factor to correct for the transfer of this variability to the most interesting signals in the sample (i.e., hit signals), the effect will obfuscate any effort to quantify biological effects of differing treatments.…”

Trends in Hit-to-Lead Optimization Following DNA-Encoded Library Screens

“…In addition, due to the presence of an attached DNA tag, any very large or highly lipophilic structures formed during DEL synthesis can be expected to stay solubilized in water during screening. Within a DEL selection for binders, initial protein–DEL stoichiometry may be skewed to avoid binding site competition effectshowever, binder identification is dependent on selection stringency and sequencing coverage, ultimately leading to preferential identification of higher affinity compounds . This is in contrast to other high-volume approaches such as HTS in which collections of compounds are screened as individual, nonlinkered structures prepared with no inherent limitations on synthetic chemistry or reaction sequence and with fewer limitations on assay formats or ranges of compound detection (Figure ).…”

“…Within a DEL selection for binders, initial protein− DEL stoichiometry may be skewed to avoid binding site competition effectshowever, binder identification is dependent on selection stringency and sequencing coverage, ultimately leading to preferential identification of higher affinity compounds. 8 This is in contrast to other high-volume approaches such as HTS in which collections of compounds are screened as individual, nonlinkered structures prepared with no inherent limitations on synthetic chemistry or reaction sequence and with fewer limitations on assay formats or ranges of compound detection (Figure 1). 9,10 A detailed comparison of screening modalities is beyond the scope of this article, and readers are referred to ref 3 for an excellent overview.…”

Recent Advances on the Selection Methods of DNA‐Encoded Libraries

“…Multiple rounds of selections can be conducted to better enrich the binders as well as align the copy number of DNA with the available sequencing capacity. For instance, larger DELs tend to have higher false negative rate in selection, [37] and sufficient sequencing coverage is an important factor; [38] researchers have explored the low limit of DNA copy for each compound, which was determined to be 10 3 ∼10 4 for large DELs [39] and 10 5 –10 6 for small DELs [34c] . It is also quite common that a non‐target protein, a denatured target, or simply “empty” beads is included in the selection to control for non‐specific binding, while parallel selections with multiple target isoforms may identify isoform‐selective binders [40] .…”