DNA Compatible Multistep Synthesis and Applications to DNA Encoded Libraries

Abstract

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.

What is a “DNA-Compatible” Reaction?

“…A handful of studies now exist describing the preparation and screening of solution-phase libraries that incorporate diverse reactions—including those rehearsed above—though only with conversion yield data. 20–23,32–34 We sought to determine whether our assay could be extensible to the investigation of solution-phase DNA-encoded reaction development, and whether and how those data could apply to solution-phase library planning and synthesis.…”

“…Conventional solution-phase library preparation includes HPLC purification, likely eliminating synthesis products attached to Pd-catalyzed DNA cleavage products (see Supporting Information). 37 The particularly aggressive pH and temperature of published DNA-compatible quinazolinone formation 34 unsurprisingly proved to be quite detrimental to encoding tag integrity (< 0.2% DNA remaining).…”

DNA‐encoded chemical libraries – achievements and remaining challenges

“…The set of reactions which can be considered for library synthesis is constantly expanding [64][65][66]. However, it is important to remember that even simple transformations (such as the formation of amide bonds) do not proceed with complete yields on 100% of substrates.…”

Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules

“…A diverse set of reactions have been successfully validated in a DNA-templated manner 36, 38 and a broader toolbox of DNA-compatible chemistry is steadily growing. 8, 39, 40 Our group has applied this concept to create libraries of DNA-templated small molecules 6 , in which the DNA tags not only function as barcodes, but also as templates that orchestrate the synthesis of each library member.…”