AbstractThe main protease (Mpro) of SARS‐CoV‐2 is a well‐characterized target for antiviral drug discovery. To date, most antiviral drug discovery efforts have focused on the S4–S1′ pocket of Mpro; however, it is still unclear whether the S1′–S3′ pocket per se can serve as a new site for drug discovery. In this study, the S1′–S3′ pocket of Mpro was found to differentially recognize viral peptidyl substrates. For instance, S3′ in Mpro strongly favors Phe or Trp, and S1′ favors Ala. The peptidyl inhibitor D‐4–77, which possesses an α‐bromoacetamide warhead, was discovered to be a promising inhibitor of Mpro, with an IC50 of 0.95 μM and an antiviral EC50 of 0.49 μM. The Mpro/inhibitor co‐crystal structure confirmed the binding mode of the inhibitor to the S1′–S3′ pocket and revealed a covalent mechanism. In addition, D‐4–77 functions as an immune protectant and suppresses SARS‐CoV‐2 Mpro‐induced antagonism of the host NF‐κB innate immune response. These findings indicate that the S1′–S3′ pocket of SARS‐CoV‐2 Mpro is druggable, and that inhibiting SARS‐CoV‐2 Mpro can simultaneously protect human innate immunity and inhibit virion assembly.
摘要
SARS-CoV-2的主要
蛋白酶(Mpro)是抗病毒药物发现的一个特征明确的靶点。迄今为止,大多数抗病毒药物的发现工作都集中在Mpro的S4-S1′口袋上;然而,S1′-S3′口袋本身能否作为药物发现的新靶点尚不清楚。本研究发现,Mpro的S1′-S3′口袋可以识别不同的病毒肽基底物。例如,Mpro 的 S3′ 极其偏爱 Phe 或 Trp,而 S1′ 则偏爱 Ala。肽基
抑制剂 D-4-77 具有α-
溴乙酰胺弹头,是一种很有前途的 Mpro
抑制剂,其 IC50 值为 0.95 μM,抗病毒
EC50 值为 0.49 μM。Mpro 与
抑制剂的共晶体结构证实了
抑制剂与 S1′-S3′ 口袋的结合模式,并揭示了共价机制。此外,D-4-77还具有免疫保护剂的功能,可抑制
SARS-CoV-2 Mpro诱导的宿主NF-κB先天免疫反应的拮抗作用。这些研究结果表明,
SARS-CoV-2 Mpro的S1′-S3′口袋是可药用的,抑制
SARS-CoV-2 Mpro可同时保护人类先天免疫和抑制病毒组装。