A method for estimating binding affinity from primary DEL selection data

• Published in: Biochemical and biophysical research communications Vol. 533; no. 2; pp. 249 - 255
• Main Authors: Chen, Qiuxia, Hall, Justin, Foley, Timothy L., Wan, Jinqiao, Li, You, Israel, David I.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 03-12-2020
• Subjects: Affinity selection; Binding Sites; Combinatorial Chemistry Techniques; DEL; DNA - chemical synthesis; DNA - chemistry; DNA encoded Library; Drug Discovery; Hit identification; Humans; Library screening; Ligands; Phosphotransferases - metabolism; Protein Binding; Small Molecule Libraries - chemical synthesis; Small Molecule Libraries - chemistry; Small Molecule Libraries - pharmacology; Library screening; LC/MS; DNA encoded Library; DEL; Affinity selection; NGS; Hit identification; PCR
• ISSN: 0006-291X; 1090-2104
• DOI: 10.1016/j.bbrc.2020.04.029

DEL selections are binding assays conducted with mixtures of chemically diverse DNA-tagged ligands and a screening target. DEL selections use DNA sequence counts to measure target binding, where ideally higher affinity ligands will have higher counts than weaker affinity ligands. However, there is not always a clear relationship between DNA sequence count (assay signal) and binding affinity. This disconnect may be due to the fidelity of library chemistry, where reactions often do not go to completion, and also to repetitive rounds of binding and elution that are standard practice in most DEL selection experiments. We describe here a strategy that addresses both of these issues and provides a means to calculate ligand affinity from primary selection data. The reaction yields of selected compounds during DEL library synthesis can also be predicted with this method.
•Method for determining compound affinity from DNA encoded library selection data.•Improvement in the effectiveness of the DEL platform for ligand discovery.•Multipoint analysis of DEL selections.