The M1 metallo‐aminopeptidase from Plasmodium falciparum, PfA‐M1, is an attractive drug target for the design of new antimalarials. Bestatin, a broad‐spectrum metalloprotease inhibitor, is a moderate inhibitor of PfA‐M1, and has been used to provide structure–activity relationships to inform drug design. The crystal structure of PfA‐M1 with bestatin bound within its active site has been determined; however, dynamics of the inhibitor and the association or dissociation pathway have yet to be characterized. Here we present an all‐atom molecular dynamics study where we have generated a hidden Markov state model from 2.3 μs of molecular dynamics simulation. Our hidden Markov state model identifies five macrostates that clearly show the events involved in bestatin dissociation from the PfA‐M1 active site. The results show for the first time that bestatin can escape the substrate specificity pockets of the enzyme, primarily due to weak interactions within the pockets. Our approach identifies relevant conformational sampling of the inhibitor inside the enzyme and the protein dynamics that could be exploited to produce potent and selective inhibitors that can differentiate between similar members of the M1 aminopeptidase superfamily.

中文翻译：

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绘制恶性疟原虫M1氨肽酶PfA-M1的Bestatin抑制途径和动力学图

恶性疟原虫的M1金属氨基肽酶Pf M-1是设计新型抗疟药的引人注目的药物靶标。Bestatin是一种广谱金属蛋白酶抑制剂，是Pf A-M1的中度抑制剂，已被用于提供构效关系以指导药物设计。Pf的晶体结构已确定在其活性位点内结合有Bestatin的A‐M1；然而，抑制剂的动力学以及缔合或解离途径尚待表征。在这里，我们介绍了一个全原子分子动力学研究，其中我们通过2.3μs的分子动力学模拟生成了一个隐马尔可夫状态模型。我们隐藏的马尔可夫状态模型确定了五个宏观状态，这些状态清楚地显示了与Pf的Bestatin解离有关的事件A‐M1活动站点。结果首次表明，牛磺酸抑制素可以逃脱酶的底物特异性口袋，这主要是由于口袋中的弱相互作用。我们的方法确定了酶内部抑制剂的相关构象取样以及可以用来产生有效和选择性抑制剂的蛋白动力学，这些抑制剂可以区分M1氨肽酶超家族的相似成员。