Rouch Catherine C, Chatterjee Arnab K, McCarty Connor, Song Lirui, Chu Alan, Johnson Kristen, Heacock Mina, Riva Laura, McNamara Case W, Wolff Karen C, Greene-Cramer Rebecca, Falco Anna De, Montelione Gaetano T, Grabovyi Gennadii A
Calibr-Skaggs Institute for Innovative Medicines, A Division of Scripps Research, La Jolla, CA 92037, USA.
Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
Bioorg Med Chem Lett. 2025 Feb 1;116:130034. doi: 10.1016/j.bmcl.2024.130034. Epub 2024 Nov 21.
The papain-like protease (PLpro) is a highly conserved domain encoded by the coronavirus (CoV) genome and it plays an essential role in the replication and maturation of the virus in addition to weakening host immune response. Due to the virus's reliance on PLpro for survival and propagation, small-molecule inhibitors of PLpro serve as an attractive model for direct-acting antiviral therapeutic agents against SARS-CoV-2. Building upon existing work aimed at designing covalent inhibitors against PLpro, we report the synthesis and structure-activity relationship of analogs based on the known covalent inhibitor 1 (Sanders, et al.2023). To evaluate the efficacy of synthesized derivatives, we conducted enzymatic inhibition assays, SARS-CoV-2/HeLa-ACE2 cellular potency and toxicity assays, and profiled the most promising analogs via in vitro ADME and in vivo pharmacokinetic studies. Additionally, we describe computational docking of profiled compounds bound to PLpro to elucidate the structure-activity relationship of compounds based on 1 and offer suggestions for optimizing the potency and selectivity of the electrophilic warhead and improving ADME and PK properties for this chemotype. Relative to the parent compound, new designs demonstrate comparable potency and target selectivity for PLpro. The accomplished SAR campaign provides novel insight for future development of antivirals against SARS-CoV-2.
木瓜蛋白酶样蛋白酶（PLpro）是冠状病毒（CoV）基因组编码的一个高度保守结构域，除了削弱宿主免疫反应外，它在病毒的复制和成熟过程中也起着至关重要的作用。由于病毒生存和繁殖依赖PLpro，PLpro的小分子抑制剂成为抗SARS-CoV-2直接作用抗病毒治疗药物的一个有吸引力的模型。基于旨在设计针对PLpro的共价抑制剂的现有工作，我们报道了基于已知共价抑制剂1（桑德斯等人，2023年）的类似物的合成及其构效关系。为了评估合成衍生物的疗效，我们进行了酶抑制试验、SARS-CoV-2/HeLa-ACE2细胞活性和毒性试验，并通过体外药物代谢及动力学和体内药代动力学研究对最有前景的类似物进行了分析。此外，我们描述了与PLpro结合的分析化合物的计算对接，以阐明基于1的化合物的构效关系，并为优化亲电弹头的效力和选择性以及改善该化学类型的药物代谢及动力学和药代动力学性质提供建议。相对于母体化合物，新设计对PLpro表现出相当的效力和靶标选择性。完成的构效关系研究为抗SARS-CoV-2抗病毒药物的未来开发提供了新见解。
