Specific anti-coronaviral drugs complementing available vaccines are urgently needed to fight the COVID-19 pandemic. Given its high conservation across the betacoronavirus genus and dissimilarity to human proteases, the SARS-CoV-2 main protease (M^pro) is an attractive drug target. SARS-CoV-2 M^pro inhibitors have been developed at unprecedented speed, most of them being substrate-derived peptidomimetics with cysteine-modifying warheads. In this study, M^pro has proven resistant towards the identification of high-affinity short substrate-derived peptides and peptidomimetics without warheads. 20 cyclic and linear substrate analogues bearing natural and unnatural residues, which were predicted by computational modelling to bind with high affinity and designed to establish structure–activity relationships, displayed no inhibitory activity at concentrations as high as 100 μM. Only a long linear peptide covering residues P₆ to P₅′ displayed moderate inhibition (K_i = 57 µM). Our detailed findings will inform current and future drug discovery campaigns targeting M^pro.

迫切需要特定的抗冠状病毒药物来补充现有疫苗，以对抗 COVID-19 大流行。鉴于其在 β 冠状病毒属中的高度保守性和与人类蛋白酶的不同性，SARS-CoV-2 主要蛋白酶 (M ^pro ) 是一个有吸引力的药物靶点。SARS-CoV-2 M ^pro抑制剂以前所未有的速度开发，其中大多数是具有半胱氨酸修饰弹头的底物衍生拟肽。在本研究中，M ^pro已证明对鉴定无弹头的高亲和力短底物衍生肽和拟肽具有抗性。20 种带有天然和非天然残基的环状和线性底物类似物在高达 100 μM 的浓度下没有显示出抑制活性，这些类似物通过计算模型预测以高亲和力结合并旨在建立结构-活性关系。_{只有覆盖残基 P 6}至 P ₅ '的长线性肽表现出中度抑制作用 ( K _i  = 57 µM)。我们的详细发现将为当前和未来针对 M ^pro的药物发现活动提供信息。