DNA-encoded chemical libraries are collections of compounds individually coupled to unique DNA tags serving as amplifiable identification barcodes. By bridging split-and-pool combinatorial synthesis with the ligation of unique encoding DNA oligomers, million- to billion-member libraries can be synthesized for use in hundreds of healthcare target screens. Although structural diversity and desirable molecular property ranges generally guide DNA-encoded chemical library design, recent reports have highlighted the utility of focused DNA-encoded chemical libraries that are structurally biased for a class of protein targets. Herein, a protease-focused DNA-encoded chemical library was designed that utilizes chemotypes known to engage conserved catalytic protease residues. The three-cycle library features functional moieties such as guanidine, which interacts strongly with aspartate of the protease catalytic triad, as well as mild electrophiles such as sulfonamide, urea, and carbamate. We developed a DNA-compatible method for guanidinylation of amines and reduction of nitriles. Employing these optimized reactions, we constructed a 9.8-million-membered DNA-encoded chemical library. Affinity selection of the library with thrombin, a common protease, revealed a number of enriched features which ultimately led to the discovery of a 1 nM inhibitor of thrombin. Thus, structurally focused DNA-encoded chemical libraries have tremendous potential to find clinically useful high-affinity hits for the rapid discovery of drugs for targets (e.g., proteases) with essential functions in infectious diseases (e.g., severe acute respiratory syndrome coronavirus 2) and relevant healthcare conditions (e.g., male contraception).

DNA编码的化学文库是化合物的集合，这些化合物分别与用作扩增识别条形码的独特DNA标签偶联。通过将分离池合并合成与独特的编码DNA低聚物连接起来，可以合成百万至十亿成员的文库，以用于数百个医疗目标筛选。尽管结构多样性和理想的分子特性范围通常指导DNA编码化学文库的设计，但最近的报道强调了聚焦于DNA编码化学文库的实用性，该结构在结构上偏向于一类蛋白质靶标。在本文中，设计了一种以蛋白酶为中心的，DNA编码的化学文库，该文库利用已知可与保守催化蛋白酶残基结合的化学型。三周期文库具有功能性部分，例如胍，它与蛋白酶催化三联体的天冬氨酸以及温和的亲电子试剂（如磺酰胺，尿素和氨基甲酸酯）强烈相互作用。我们开发了一种DNA兼容的方法，用于胺的胍基化和腈的还原。利用这些优化的反应，我们构建了一个980万成员的DNA编码化学文库。与凝血酶（一种常见的蛋白酶）对文库的亲和力选择揭示了许多丰富的功能，这些功能最终导致发现了1 nM凝血酶抑制剂。因此，以结构为重点的DNA编码的化学文库具有巨大的潜力，可找到临床上有用的高亲和力命中物，以快速发现具有传染病（例如严重急性呼吸综合征冠状病毒2）必需功能的靶标药物（例如蛋白酶）和相关的医疗条件（例如，