Antiviral agents that complement vaccination are urgently needed to end the COVID-19 pandemic. The SARS-CoV-2 papain-like protease (PLpro), one of only two essential cysteine proteases that regulate viral replication, also dysregulates host immune sensing by binding and deubiquitination of host protein substrates. PLpro is a promising therapeutic target, albeit challenging owing to featureless P1 and P2 sites recognizing glycine. To overcome this challenge, we leveraged the cooperativity of multiple shallow binding sites on the PLpro surface, yielding novel 2-phenylthiophenes with nanomolar inhibitory potency. New cocrystal structures confirmed that ligand binding induces new interactions with PLpro: by closing of the BL2 loop of PLpro forming a novel “BL2 groove” and by mimicking the binding interaction of ubiquitin with Glu167 of PLpro. Together, this binding cooperativity translates to the most potent PLpro inhibitors reported to date, with slow off-rates, improved binding affinities, and low micromolar antiviral potency in SARS-CoV-2-infected human cells.

中文翻译：

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利用结合协同性设计用于 COVID-19 抗病毒治疗的 SARS-CoV-2 PLpro 抑制剂

为了结束 COVID-19 大流行，迫切需要补充疫苗接种的抗病毒药物。SARS-CoV-2 木瓜蛋白酶样蛋白酶 (PLpro) 是调节病毒复制的仅有的两种必需半胱氨酸蛋白酶之一，也通过宿主蛋白底物的结合和去泛素化来失调宿主免疫感应。PLpro 是一个有前途的治疗靶点，尽管由于识别甘氨酸的 P1 和 P2 位点无特征而具有挑战性。为了克服这一挑战，我们利用 PLpro 表面上多个浅结合位点的协同作用，产生具有纳摩尔抑制效力的新型 2-苯基噻吩。新的共晶结构证实配体结合诱导与 PLpro 的新相互作用：通过关闭 PLpro 的 BL2 环形成新的“BL2 凹槽”，并模拟泛素与 PLpro 的 Glu167 的结合相互作用。总之，这种结合协同性转化为迄今为止报道的最有效的 PLpro 抑制剂，在 SARS-CoV-2 感染的人类细胞中具有缓慢的解离速率、改善的结合亲和力和低微摩尔抗病毒效力。