Quantitative Comparison of Enrichment from DNA-Encoded Chemical Library Selections

Abstract

DNA-encoded chemical libraries (DELs) provide a high-throughput and cost-effective route for screening billions of unique molecules for binding affinity for diverse protein targets. Identifying candidate compounds from these libraries involves affinity selection, DNA sequencing, and measuring enrichment in a sample pool of DNA barcodes. Successful detection of potent binders is affected by many factors, including selection parameters, chemical yields, library amplification, sequencing depth, sequencing errors, library sizes, and the chosen enrichment metric. To date, there has not been a clear consensus about how enrichment from DEL selections should be measured or reported. We propose a normalized z-score enrichment metric using a binomial distribution model that satisfies important criteria that are relevant for analysis of DEL selection data. The introduced metric is robust with respect to library diversity and sampling and allows for quantitative comparisons of enrichment of n-synthons from parallel DEL selections. These features enable a comparative enrichment analysis strategy that can provide valuable information about hit compounds in early stage drug discovery.

Discovery of potent thrombin inhibitors from a protease-focused DNA-encoded chemical library

“…The enrichment of n-synthons (i.e., the encoded association of a chemical building block and unique DNA sequence) for thrombin in comparison with NTC were plotted ( Fig. 5 A ) ( 36 ). The enrichment of each n-synthon was measured using a normalized z-score metric.…”

DNA Encoded Libraries: A Visitor's Guide

“…Unfortunately, experimental parameters such as panning/incubation conditions, washing procedures, detergent load, and protein immobilization procedures have been shown to profoundly impact the selection outcome. [27,38] As such, no general method exists, and Although the affinity selection procedure described above has proven useful for identifying hits in numerous DEL campaigns, the empirical nature of the selection is not applicable to many relevant classes of proteins because a soluble, isolated, and purified protein is required. [31] One advance towards expanding the proteome available for DEL selections is the recently reported cell-based DEL screen ( Figure 3B).…”

“…The protein can be immobilized before or after the panning step and multiple wash and elute conditions have been described. Unfortunately, experimental parameters such as panning/incubation conditions, washing procedures, detergent load, and protein immobilization procedures have been shown to profoundly impact the selection outcome . As such, no general method exists, and experimental systems are usually optimized for each protein of interest.…”

Evolving a Peptide: Library Platforms and Diversification Strategies

“…Furthermore, DEL platforms are compatible with parallel screening against multiple targets, enable activity-agnostic screening for identification of "silent binders", and consume relatively low amounts of reagents [54]. In addition, not only individual screening hits are identified, but rather, larger families can be detected, in which related building blocks or combinations thereof are enriched [59]. Limitations of the platform include possible interference of the oligonucleotide tag in target-binder interaction that may cause steric hindrance.…”