insight

Simulated screening of DNA encoded libraries indicates that the presence of truncated byproducts complicates the relationship between library member enrichment and equilibrium association constant (these truncates result from incomplete chemical reactions during library synthesis). Further, simulations indicate that some patterns observed in reported experimental data may result from the presence of truncated byproducts in the library mixture and not structure–activity relationships. Potential experimental methods of minimizing the presence of truncates are assessed via simulation; the relationship between enrichment and equilibrium association constant for libraries of differing purities is investigated. Data aggregation techniques are demonstrated that allow for more accurate analysis of screening results, in particular when the screened library contains significant quantities of truncates.

DNA encoded library screens have gained recent interest as they allow for screening of millions of small molecules in a simple manner, with the goal of providing novel chemical starting points in target-based hit identification. Despite this interest, no publication describes the physical properties, novelty, or structural diversity of molecules derived from such screens, nor a comparison of productivity of different DNA encoded libraries. Here we address this gap by analysis of two DNA encoded library screens run against two protein targets employing mixtures of up to 16 different libraries. Fifty-seven exemplar small molecule compounds from 34 structurally distinct clusters were prioritized from the screening results, synthesized and tested for biochemical activity. Thirty-five of the 57 compounds possess significant biochemical activity (IC50 ≤ 10 μM). Seventeen of the 35 biochemically active compounds possess a molecular weight (MW) < 500 Dalton (Da) and clogP< 5, and 6 possess a MW < 400 Da and clogP< 4. None of the 57 DEL-derived compounds exist in the Roche corporate high throughput screening collection and public compound collections. Productivity per library was observed to be independent of library size. The most productive of the 16 investigated libraries was synthesized employing only simple chemistry. Physical properties of DEL-derived compounds correlate with average library properties when truncated sub-libraries are accounted for. Our analysis may help guide the design of future DNA encoded libraries.

Complex mixtures of DNA encoded small molecules may be readily interrogated via high-throughput sequencing. These DNA encoded libraries (DELs) are commonly used to discover molecules that interact with pharmaceutically relevant proteins. The chemical diversity displayed by the library is key to successful discovery of potent, novel, and drug-like chemical matter. The small molecule moieties of DELs are generally synthesized though a multistep process, and each chemical step is accomplished while it is simultaneously attached to an encoding DNA oligomer. Hence, library chemical diversity is often limited to DNA compatible synthetic reactions. Herein, protocols for 24 reactions are provided that have been optimized for high-throughput production of DELs. These protocols detail the multistep synthesis of benzimidazoles, imidazolidinones, quinazolinones, isoindolinones, thiazoles, and imidazopyridines. Additionally, protocols are provided for a diverse range of useful chemical reactions including BOC deprotection (under pH neutral conditions), carbamylation, and Sonogashira coupling. Last, step-by-step protocols for synthesizing functionalized DELs from trichloronitropyrimidine and trichloropyrimidine scaffolds are detailed.