There is a clinical need for direct-acting antivirals targeting SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, to complement current therapeutic strategies. The main protease (M^pro) is an attractive target for antiviral therapy. However, the vast majority of protease inhibitors described thus far are peptidomimetic and bind to the active-site cysteine via a covalent adduct, which is generally pharmacokinetically unfavorable. We have reported the optimization of an existing FDA-approved chemical scaffold, perampanel, to bind to and inhibit M^pro noncovalently with IC₅₀s in the low-nanomolar range and EC₅₀s in the low-micromolar range. Here, we present nine crystal structures of M^pro bound to a series of perampanel analogs, providing detailed structural insights into their mechanism of action and structure-activity relationship. These insights further reveal strategies for pursuing rational inhibitor design efforts in the context of considerable active-site flexibility and potential resistance mechanisms.

临床需要针对 SARS-CoV-2（导致 COVID-19 大流行的冠状病毒）的直接作用抗病毒药物，以补充当前的治疗策略。主要蛋白酶 (M ^pro ) 是抗病毒治疗的一个有吸引力的靶点。然而，迄今为止描述的绝大多数蛋白酶抑制剂都是肽模拟物，并通过共价加合物与活性位点半胱氨酸结合，这通常在药代动力学上是不利的。我们报道了 FDA 批准的现有化学支架吡仑帕奈的优化，以非共价结合并抑制 M ^pro ，IC ₅₀处于低纳摩尔范围，EC ₅₀处于低微摩尔范围。在这里，我们展示了 M ^pro与一系列吡仑帕奈类似物结合的九种晶体结构，为它们的作用机制和构效关系提供了详细的结构见解。这些见解进一步揭示了在相当大的活​​性位点灵活性和潜在耐药机制的背景下追求合理抑制剂设计工作的策略。