McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA.
Infectious Disease Assay Development Laboratory/HTS, University of Kansas, Lawrence, KS 66047, USA.
Bioorg Med Chem. 2022 Aug 1;67:116788. doi: 10.1016/j.bmc.2022.116788. Epub 2022 May 11.
A series of amino acid based 7H-pyrrolo[2,3-d]pyrimidines were designed and synthesized to discern the structure activity relationships against the SARS-CoV-2 nsp3 macrodomain (Mac1), an ADP-ribosylhydrolase that is critical for coronavirus replication and pathogenesis. Structure activity studies identified compound 15c as a low-micromolar inhibitor of Mac1 in two ADP-ribose binding assays. This compound also demonstrated inhibition in an enzymatic assay of Mac1 and displayed a thermal shift comparable to ADPr in the melting temperature of Mac1 supporting binding to the target protein. A structural model reproducibly predicted a binding mode where the pyrrolo pyrimidine forms a hydrogen bonding network with Asp and the amide backbone NH of Ile in the adenosine binding pocket and the carboxylate forms hydrogen bonds to the amide backbone of Phe and Asp, part of the oxyanion subsite of Mac1. Compound 15c also demonstrated notable selectivity for coronavirus macrodomains when tested against a panel of ADP-ribose binding proteins. Together, this study identified several low MW, low µM Mac1 inhibitors to use as small molecule chemical probes for this potential anti-viral target and offers starting points for further optimization.
设计并合成了一系列基于氨基酸的 7H-吡咯并[2,3-d]嘧啶，以区分其针对 SARS-CoV-2 nsp3 结构域（Mac1）的结构活性关系，Mac1 是一种 ADP-核糖基水解酶，对冠状病毒的复制和发病机制至关重要。结构活性研究发现，化合物 15c 在两种 ADP-核糖结合测定中是 Mac1 的低微摩尔抑制剂。该化合物在 Mac1 的酶测定中也显示出抑制作用，并且在 Mac1 的熔点的热移位与 ADPr 相当，支持与靶蛋白结合。结构模型可重现性地预测了一种结合模式，其中吡咯并嘧啶与天冬氨酸形成氢键网络，酰胺主链 NH 与 Ile 在腺苷结合口袋中，羧基与 Phe 和 Asp 的酰胺主链形成氢键，这是 Mac1 的氧阴离子亚基的一部分。化合物 15c 在针对一组 ADP-核糖结合蛋白的测试中也表现出对冠状病毒结构域的显著选择性。总的来说，这项研究确定了几种低 MW、低 µM 的 Mac1 抑制剂，可作为该潜在抗病毒靶标的小分子化学探针，并为进一步优化提供了起点。
