Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA.
Medical Scientist Training Program, Columbia University Irving Medical Center, New York, New York, USA.
J Virol. 2021 Jun 24;95(14):e0237420. doi: 10.1128/JVI.02374-20.
We describe a mammalian cell-based assay to identify coronavirus 3CL protease (3CLpro) inhibitors. This assay is based on rescuing protease-mediated cytotoxicity and does not require live virus. By enabling the facile testing of compounds across a range of 15 distantly related coronavirus 3CLpro enzymes, we identified compounds with broad 3CLpro-inhibitory activity. We also adapted the assay for use in compound screening and in doing so uncovered additional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3CLpro inhibitors. We observed strong concordance between data emerging from this assay and those obtained from live-virus testing. The reported approach democratizes the testing of 3CLpro inhibitors by developing a simplified method for identifying coronavirus 3CLpro inhibitors that can be used by the majority of laboratories, rather than the few with extensive biosafety infrastructure. We identified two lead compounds, GC376 and compound 4, with broad activity against all 3CL proteases tested, including 3CLpro enzymes from understudied zoonotic coronaviruses. Multiple coronavirus pandemics have occurred over the last 2 decades. This has highlighted a need to be proactive in the development of therapeutics that can be readily deployed in the case of future coronavirus pandemics. We developed and validated a simplified cell-based assay for the identification of chemical inhibitors of 3CL proteases encoded by a wide range of coronaviruses. This assay is reporter free, does not require specialized biocontainment, and is optimized for performance in high-throughput screening. By testing reported 3CL protease inhibitors against a large collection of 3CL proteases with variable sequence similarity, we identified compounds with broad activity against 3CL proteases and uncovered structural insights into features that contribute to their broad activity. Furthermore, we demonstrated that this assay is suitable for identifying chemical inhibitors of proteases from families other than 3CL proteases.
我们描述了一种基于哺乳动物细胞的测定方法,用于鉴定冠状病毒 3CL 蛋白酶(3CLpro)抑制剂。该测定法基于挽救蛋白酶介导的细胞毒性,而不需要活病毒。通过使化合物在 15 种不同冠状病毒 3CLpro 酶的广泛范围内进行易于测试,我们鉴定出具有广泛 3CLpro 抑制活性的化合物。我们还使该测定法适应于化合物筛选,并在此过程中发现了其他严重急性呼吸综合征冠状病毒 2(SARS-CoV-2)3CLpro 抑制剂。我们观察到,从该测定法中获得的数据与从活病毒测试中获得的数据之间具有很强的一致性。该方法通过开发一种用于鉴定冠状病毒 3CLpro 抑制剂的简化方法,使大多数实验室而不是具有广泛生物安全基础设施的少数实验室能够进行 3CLpro 抑制剂的测试,从而使 3CLpro 抑制剂的测试民主化。我们鉴定出两种先导化合物 GC376 和化合物 4,它们对所有测试的 3CL 蛋白酶均具有广泛的活性,包括来自研究较少的人畜共患冠状病毒的 3CLpro 酶。在过去的 20 年中,已经发生了多次冠状病毒大流行。这突显了需要积极开发可在未来冠状病毒大流行中迅速部署的治疗方法。我们开发并验证了一种简化的基于细胞的测定法,用于鉴定广泛的冠状病毒编码的 3CL 蛋白酶的化学抑制剂。该测定法无报告基因,不需要专门的生物安全设施,并且针对高通量筛选进行了优化。通过用大量具有不同序列相似性的 3CL 蛋白酶对报告的 3CL 蛋白酶抑制剂进行测试,我们鉴定出了对 3CL 蛋白酶具有广泛活性的化合物,并深入了解了对其广泛活性有贡献的结构特征。此外,我们证明该测定法适合于鉴定来自 3CL 蛋白酶以外的家族的蛋白酶的化学抑制剂。