Abstract：
Main proteases (Mpros) are a class of conserved cysteine hydrolases among coronaviruses and play a crucial role in viral replication. Therefore, Mpros are ideal targets for the development of pan-coronavirus drugs. X77, previously developed against SARS-CoV Mpro, was repurposed as a non-covalent tight binder inhibitor against SARS-CoV-2 Mpro during COVID-19 pandemic. Many novel inhibitors with favorable efficacy have been discovered using X77 as a reference, suggesting that X77 could be a valuable scaffold for drug design. However, the broad-spectrum performance of X77 and underlying mechanism remain less understood. Here, we reported the crystal structures of Mpros from SARS-CoV-2, SARS-CoV, and MERS-CoV, and several Mpro mutants from SARS-CoV-2 variants bound to X77. A detailed analysis of these structures revealed key structural determinants essential for interaction and elucidated the binding modes of X77 with different coronaviral Mpros. The potencies of X77 against these investigated Mpros were further evaluated through molecular dynamic simulation and binding free energy calculation. These data provide molecular insights into broad-spectrum inhibition against coronaviral Mpros by X77 and the similarities and differences of X77 when bound to various Mpros, which will promote X77-based design of novel antivirals with broad-spectrum efficacy against different coronaviruses and SARS-CoV-2 variants.
摘要：
主要蛋白酶（Mpros）是冠状病毒中一类保守的半胱氨酸水解酶，在病毒复制中起着至关重要的作用。因此,MPRs是开发泛冠状病毒药物的理想目标。X77，以前针对SARS-CoVMpro开发的，在COVID-19大流行期间被重新用作抗SARS-CoV-2Mpro的非共价紧密结合剂抑制剂。使用X77作为参考，已经发现了许多具有良好功效的新型抑制剂。这表明X77的结构可能是药物设计的有价值的支架。然而,X77的广谱性能和潜在机制仍然知之甚少。这里,我们报道了SARS-CoV-2，SARS-CoV，还有MERS-CoV,和几个来自SARS-CoV-2变体的Mpro突变体与X77结合。对这些结构的详细分析揭示了相互作用所必需的关键结构决定因素，并阐明了X77与不同冠状病毒Mpro的结合模式。通过分子动力学模拟和结合自由能计算进一步评估X77对这些研究的Mpros的效力。这些数据提供了对X77对冠状病毒Mpros的广谱抑制的分子见解，以及X77与各种Mpros结合时的异同。这将促进基于X77的新型抗病毒药物的设计，具有针对不同冠状病毒和SARS-CoV-2变体的广谱功效。
