DNA-encoded chemical libraries (DECLs) are a powerful tool for target-directed hit discovery. By bridging split-and-pool combinatorial synthetic approaches with the ligation of unique encoding DNA oligomers, million to billion member libraries may be synthesized at micromole scales for use in hundreds of target screens. Although DECLs are often used generically within a screening pipeline, recent reports have highlighted the utility of focused DECLs that are structurally biased for a particular class of protein targets. As focused DECL designs require prior structural and mechanistic information on both the targets and their known small molecule inhibitors, they are best suited for well-studied target classes such as proteases. A common strategy of many known protease inhibitors has been to interact with aspartate in the catalytic triad through the inclusion of a positively-charged guanidine moiety. To exploit this strategy within a DECL screen, we initiated studies to develop a DNA-compatible guanidinylation for aliphatic and aromatic amines. Within this study, a number of commercially available guanidinylation reagents and various DNA-relevant reaction conditions were screened. Ultimately we found primary and unhindered secondary aliphatic amines undergo full conversion to free guanidine with reagent N-Boc-1H-pyrazole-1-carboxamidine, whereas electron deficient aliphatic amines and anilines gave better conversion with a similar but more reactive reagent N-Boc-N’-TFA-pyrazole-1-carboxamidine. After evaluation of substrate scope and DNA-stability, our optimized guanidinylation conditions were applied within the production of a focused DECL of nine million compounds. In addition to the guanidine moiety, this DECL also featured mildly electrophilic groups such as sulfonamide, urea, and carbamate, often found in protease inhibitors. This library was then utilized in single and multi-round selection experiments against two proteases, thrombin and trypsin, revealing potential hits that are currently being synthesized for in vitro evaluation.

Optimization of guanidinylation of amines for the synthesis of protease-focused DNA-encoded chemical library

2019 Fall National Meeting

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